A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

abisolid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
AbortLoadIndexPageController - Class in net.sourceforge.solexatools.webapp.controller
 
AbortLoadIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController
 
abortTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
abortTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
AbstractInMemoryPlugin - Class in com.github.seqware.queryengine.plugins.inmemory
Base class for all in-memory plug-ins
AbstractInMemoryPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
AbstractInMemorySet<S extends MolSetInterface,T> - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a MolSetInterface.
AbstractInMemorySet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
AbstractMolSet<S extends MolSetInterface> - Class in com.github.seqware.queryengine.model.impl
Implements TTL behaviour for sets
AbstractMolSet() - Constructor for class com.github.seqware.queryengine.model.impl.AbstractMolSet
 
AbstractMRHBaseBatchedPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr
This plug-in abstracts plug-ins that use a model manager to keep track of Features that "pass" the mapper
AbstractMRHBaseBatchedPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBaseBatchedPlugin
 
AbstractMRHBasePlugin<ReturnType> - Class in com.github.seqware.queryengine.plugins.hbasemr
Abstract implementation of an abstract map/reduce-based plug-in for a HBase back-end.
AbstractMRHBasePlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
AbstractMRInMemoryPlugin - Class in com.github.seqware.queryengine.plugins.inmemory
Base class for all in-memory plug-ins that do MR
AbstractMRInMemoryPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.AbstractMRInMemoryPlugin
 
AbstractScanInMemoryPlugin - Class in com.github.seqware.queryengine.plugins.inmemory
Base class for all in-memory plug-ins that do Scan
AbstractScanInMemoryPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.AbstractScanInMemoryPlugin
 
abundancemeasurement - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
accept(Representation) - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
ACCESSION_ONLY - Static variable in class com.github.seqware.queryengine.system.importers.OBOImporter
Determines whether we use "acccession-only" tags.
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
ACL - Class in com.github.seqware.queryengine.model.interfaces
Access control list that determines permissions and access rights to features and feature sets.
ACL.Builder - Class in com.github.seqware.queryengine.model.interfaces
 
ACL.Builder() - Constructor for class com.github.seqware.queryengine.model.interfaces.ACL.Builder
 
ACL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
ACLable - Interface in com.github.seqware.queryengine.model.interfaces
Interface for object under access control.
action - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS
 
actions - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
Adag - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus.object
 
Adag(Workflow) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Adag
 
adapterCont - Class in net.sourceforge.seqware.pipeline.modules.qc
Basic QC report This module parses quality report from Illumina pipeline (Gerald) PE Adapters1 5' P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT PE PCR Primer 1.01 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3 PE PCR Primer 2.01 5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT PE Read 1 Sequencing Primer 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT PE Read 2 Sequencing Primer 5' CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT (1) Normally, PE read 2 is used for SE sequencing and 1st of PE in PE run and (2)PE read 1 will is used for 2nd of PE in PE run Underlying script: sw_module_adapterCont.pl (by Sara Grimm) Newly updated script: calculate_adapter_contamination.pl (by Sara Grimm) 6/2/2010 Necessary programs: perl Expected output: adapter_cont.txt
adapterCont() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
 
adapterspec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
 
add(Feature) - Method in class com.github.seqware.queryengine.model.FeatureSet
Adds a single new Feature to the set.
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.FeatureSet
Adds a collection of new Feature to the set.
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.FeatureList
 
add(T) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
add(Collection<T>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
add(T...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
add(Feature...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
add(Tag) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
add(Collection<Tag>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
add(Tag...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
add(Feature...) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
add(T) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Add one element to the set
add(Collection<T>) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Add numerous elements from within a set
add(T...) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Add an array of elements
add(Integer, FileAttribute) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
 
add(Integer, FileAttribute) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
 
add(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
 
add(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
 
add(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
 
add(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
 
add(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
 
add(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
 
add(Experiment) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
 
add(File) - Method in class net.sourceforge.seqware.common.model.lists.FileList
 
add(IUS) - Method in class net.sourceforge.seqware.common.model.lists.IUSList
 
add(Lane) - Method in class net.sourceforge.seqware.common.model.lists.LaneList
 
add(Processing) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
 
add(ReturnValue) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
 
add(Sample) - Method in class net.sourceforge.seqware.common.model.lists.SampleList
 
add(SequencerRun) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
 
add(Study) - Method in class net.sourceforge.seqware.common.model.lists.StudyList
 
add(Workflow) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
 
add(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
 
add(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
 
add(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
 
add(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
 
add(String, String) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
 
add - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
add_empty_processing_event(int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
add_empty_processing_event_by_parent_accession(int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
add_task_group(int[], int[], String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
add_workflow_run(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
add_workflow_run_ancestor(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
addACL(ACL) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addAllAnalysisIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
addAllFeatures(Iterable<? extends QueryEngine.FeaturePB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addAllFeatures(Iterable<? extends QESupporting.FSGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addAllFeatureSetIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addAllGrps(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addAllReferenceIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addAllRights(Iterable<? extends Boolean>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
addAllTags(Iterable<? extends QESupporting.TagPB>) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addAllTags(Iterable<? extends QESupporting.TagPB>) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addAllTagSpecIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addAllUsers(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addAnalysisIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
addAnalysisIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
addAnalysisIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
addAnalysisIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
addAnalysisIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
addAnalysisIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
addAnalysisPlugin(AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addAnalysisSet(AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addArgument(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
 
addArgumentPair(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
 
addAttribute(AttributeDto) - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
 
addAttribute(AttributeDto) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
 
addCommandInput(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
addExperiment(Integer, Integer, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
TODO: this needs to setup rows in experiment_library_design and experiment_spot_design
addFeatures(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeatures(int, QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeatures(QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeatures(int, QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeatures(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeatures(int, QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeatures(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeatures(int, QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeaturesBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeaturesBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeatureSet(FeatureSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addFeatureSetIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addGroup(Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addGrps(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrps(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrps(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrps(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrpsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrpsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addJob(Job) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
addJob(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Adag
 
addJobArgument(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
addModuleArgument(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
addModuleArgument(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
addModuleOption(Argument) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Arguments
 
addModuleOption(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Arguments
 
addParent(Job) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
addParent(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
addProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.Lane
 
addProcessings(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
 
addProfile(JobProfile) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
addReference(Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addReferenceIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceSet(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
AddRGTags - Class in net.sourceforge.seqware.pipeline.modules.BamFilters
Annotate BAM file with read group tags.
AddRGTags() - Constructor for class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
 
addRights(boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
addRow(Flexigrid.Cells) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
addSample(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
addSample(Integer, Integer, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
addSample(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
addSample(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
TODO: this needs to setup rows in experiment_library_design and experiment_spot_design
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
addStudy(String, String, String, StudyType, String, String, Integer) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
addSysOption(Argument) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Arguments
 
addSysOption(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Arguments
 
addTag(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
addTag(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
addTags(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTags(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTags(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTags(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
addTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
addTagsBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTagsBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTagSet(TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addTagSpecIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addUser(User) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addUsers(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsers(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsers(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsers(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsersBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsersBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUserToGroup(User, Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
addWorkflowRun(String, String, String) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
addWorkflowRunParam(int, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
ADHOC_TAGSETS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
adhoctagset - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
algorithm - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
algorithmName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
AlignmentQualityReportDecider - Class in net.sourceforge.seqware.pipeline.deciders
FIXME: this extends the plugin but really it should be a decider subclass.
AlignmentQualityReportDecider() - Constructor for class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
 
alignStat - Class in net.sourceforge.seqware.pipeline.modules.qc
Performing post alignment per lane based counting Underlying script: sw_module_alignStat.pl Necessary programs: perl, java, Picard (SamFormatConverter.jar) Output: ~.mapped.txt tab-delimited files in four columns: bam file name, raw read count, mapped read count and aligned percentage (%)
alignStat() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.alignStat
 
AnalisysBulkDownloadListController - Class in net.sourceforge.solexatools.webapp.controller
 
AnalisysBulkDownloadListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
 
AnalisysBulkDownloadListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
 
AnalisysBulkDownloadListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
AnalisysEventController - Class in net.sourceforge.solexatools.webapp.controller
StudyController
AnalisysEventController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
 
AnalisysEventController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
 
AnalisysListController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
AnalisysListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysListController
 
AnalisysListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
 
AnalisysListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
AnalisysRunningListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
 
AnalisysRunningListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
Analysis<ReturnType> - Class in com.github.seqware.queryengine.model
An Analysis object represents specific calls to analysis components, most of which will be implemented as an analysis plug-in on the backend.
Analysis() - Constructor for class com.github.seqware.queryengine.model.Analysis
Create a new analysis
analysis - Variable in class com.github.seqware.queryengine.model.Analysis.Builder
 
analysis - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet
 
Analysis.Builder - Class in com.github.seqware.queryengine.model
 
Analysis.Builder() - Constructor for class com.github.seqware.queryengine.model.Analysis.Builder
 
ANALYSIS_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
 
analysisattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES
 
analysisattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
analysisCenter - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
analysisfiles - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
ANALYSISIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
AnalysisIO - Class in com.github.seqware.queryengine.impl.protobufIO
Place-holder
AnalysisIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.AnalysisIO
 
analysislink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS
 
analysislinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
AnalysisPluginInterface<T> - Interface in com.github.seqware.queryengine.plugins
This will describe the interface custom plugins must conform to.
AnalysisPluginInterface.ReturnValue - Class in com.github.seqware.queryengine.plugins
 
AnalysisPluginInterface.ReturnValue() - Constructor for class com.github.seqware.queryengine.plugins.AnalysisPluginInterface.ReturnValue
 
AnalysisSet - Interface in com.github.seqware.queryengine.model
An AnalysisSet object groups analysis events that are created by software suites or related tools.
AnalysisSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet
 
AnalysisSet.Builder - Class in com.github.seqware.queryengine.model
 
AnalysisSet.Builder() - Constructor for class com.github.seqware.queryengine.model.AnalysisSet.Builder
 
AnalysisSetIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
AnalysisSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.AnalysisSetIO
 
AnalysisType - Class in net.sourceforge.seqware.queryengine.webservice.model
A SRA analysis object captures secondary analysis results from a short read dataset.
AnalysisType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
analysistype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
AnalysisType.ANALYSISATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES
 
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
 
AnalysisType.ANALYSISFILES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISFILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES
 
AnalysisType.ANALYSISFILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISFILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
 
AnalysisType.ANALYSISLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS
 
AnalysisType.ANALYSISLINKS.ANALYSISLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
 
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
 
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
 
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
 
AnalysisType.ANALYSISTYPE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISTYPE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
AnalysisType.PARENT - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
AnalysisType.PARENT.EXPERIMENTREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.EXPERIMENTREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
 
AnalysisType.PARENT.RUNREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.RUNREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
 
AnalysisType.PARENT.SAMPLEPOOLREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEPOOLREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF
 
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
 
AnalysisType.PARENT.SAMPLEREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
 
AnalysisType.PARENT.STUDYREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.STUDYREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
 
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateExperiment(int, Set<ExperimentAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateIUS(int, IUSAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateIUS(int, Set<IUSAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateLane(int, LaneAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateLane(int, Set<LaneAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateProcessing(int, Set<ProcessingAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateSample(int, SampleAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateSample(int, Set<SampleAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateStudy(int, StudyAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateStudy(int, Set<StudyAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
AnnotateVariantDB - Class in net.sourceforge.seqware.pipeline.modules.queryengine
Purpose: This module uses the VariantConsequenceImporter and TagAnnotationImporter from the SeqWare QueryEngine Backend project to annotate with coding consequence and dbSNP status.
AnnotateVariantDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
AnnotateVariantsWithContigAndZygosity - Class in net.sourceforge.seqware.queryengine.tools.annotators
 
AnnotateVariantsWithContigAndZygosity() - Constructor for class net.sourceforge.seqware.queryengine.tools.annotators.AnnotateVariantsWithContigAndZygosity
 
AnnotateWithCodingConsequence - Class in net.sourceforge.seqware.pipeline.modules.queryengine
Purpose: This module uses perl annotation scripts from SeqWare Pipeline to annotate with coding consequence status and then generates annotations tag files for loading in the database.
AnnotateWithCodingConsequence() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
AnnotateWithDbSNP - Class in net.sourceforge.seqware.pipeline.modules.queryengine
Purpose: This module uses an existing variant database, dumps the variants as a BED file, uses perl annotation scripts from SeqWare Pipeline to annotate with dbSNP status, and create a load file that can be loaded back into the DB.
AnnotateWithDbSNP() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
annotationAwareAspectJAutoProxyCreator() - Method in class net.sourceforge.seqware.pipeline.runner.Runner2.ModuleConfig
 
anonymizedname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
 
ApacheSerialization - Class in com.github.seqware.queryengine.impl
 
ApacheSerialization() - Constructor for class com.github.seqware.queryengine.impl.ApacheSerialization
 
APP - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
 
Argument - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
Argument(String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
 
argument - Variable in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
Arguments - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus.object
 
Arguments() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Arguments
 
ArgumentUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus
 
ArgumentUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.ArgumentUtils
 
asDto(SampleSearch) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
asDto(Attribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
asDto(Registration) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
asDto(Sample) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
asDto(IUS) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
asDto(File) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
aSet - Variable in class com.github.seqware.queryengine.model.AnalysisSet.Builder
 
aSet - Variable in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
aSet - Variable in class com.github.seqware.queryengine.model.Group.Builder
 
aSet - Variable in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
aSet - Variable in class com.github.seqware.queryengine.model.TagSet.Builder
 
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
associateTag(Tag) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
associateTag(Tag) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
associate new tag to a subject with a null value and a null predicate
associateTag(Tag) - Method in class com.github.seqware.queryengine.model.Tag
Tags are not taggable, but it is actually easier to have the capability via inheritance and just turn it off
atDto(Organism) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
Atom<T extends Atom> - Interface in com.github.seqware.queryengine.model
Implements core functionality that is shared by all classes that require tags.
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
AtomImpl<T extends Atom> - Class in com.github.seqware.queryengine.model.impl
Implements core functionality that is shared by all classes that require tags.
AtomImpl() - Constructor for class com.github.seqware.queryengine.model.impl.AtomImpl
 
atomStateChange(Atom, CreateUpdateManager.State) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Called by Atoms when they need to change state (for example, to notify that they have become a dirty new version)
atomStateChange(Atom, CreateUpdateManager.State) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
Attribute - Interface in net.sourceforge.seqware.common.model
 
attribute - Variable in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
 
AttributeAnnotator - Class in net.sourceforge.seqware.pipeline.plugins
 
AttributeAnnotator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
 
AttributeDto - Class in net.sourceforge.seqware.webservice.dto
 
AttributeDto() - Constructor for class net.sourceforge.seqware.webservice.dto.AttributeDto
 
attributes - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
authenticate() - Method in class net.sourceforge.seqware.webservice.resources.BasicResource
 
authenticate(String) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
Authentication - Class in net.sourceforge.solexatools.authentication
 
Authentication() - Constructor for class net.sourceforge.solexatools.authentication.Authentication
 
AUTOFLUSH - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
available - Variable in class com.github.seqware.queryengine.system.importers.Importer
 
available - Variable in class net.sourceforge.seqware.queryengine.tools.importers.Importer
 

B

BackEndInterface - Interface in com.github.seqware.queryengine.impl
This interface specifies operations to persist, update, and add objects to the back-end without knowing about the specific database back-end.
BackendPool - Class in net.sourceforge.seqware.queryengine.webservice.model
 
BackendPool() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
 
BadFile - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
 
BadModule - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
 
BadParameter - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
 
BadRunnerParams - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
 
BAM2Count - Class in net.sourceforge.seqware.pipeline.modules.quantification
Get gene level count from BAM file.
BAM2Count() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
 
barcodeSeqence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
 
BaseBuilder<S,T extends BaseBuilder> - Class in com.github.seqware.queryengine.model.interfaces
Builders are used to construct Atom.
BaseBuilder() - Constructor for class com.github.seqware.queryengine.model.interfaces.BaseBuilder
 
basecaller - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
 
basecalls - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
 
basecoord - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
baseQualities - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
BasicDecider - Class in net.sourceforge.seqware.pipeline.deciders
 
BasicDecider() - Constructor for class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
basicQC - Class in net.sourceforge.seqware.pipeline.modules.qc
Purpose: This module generates pre and post alignment QC reports using dqc from the DNAA package.
basicQC() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.basicQC
 
BasicResource - Class in net.sourceforge.seqware.webservice.resources
See https://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_extend_the_web_service#Basic_Resource
BasicResource() - Constructor for class net.sourceforge.seqware.webservice.resources.BasicResource
 
BasicRestlet - Class in net.sourceforge.seqware.webservice.resources
See https://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_extend_the_web_service#Basic_Resource
BasicRestlet(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
BasicWorkflow - Class in net.sourceforge.seqware.pipeline.workflow
 
BasicWorkflow(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
BasicWorkflow.Job - Enum in net.sourceforge.seqware.pipeline.workflow
 
BATCH_SIZE - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
batch_size - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
BATCH_SIZE_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
BCtrend - Class in net.sourceforge.seqware.pipeline.modules.qc
Performing per lane based statistics Underlying script: sw_module_BCtrend.pl Necessary programs: perl Expected output: read_depth.txt
BCtrend() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
 
BeanFactory - Class in net.sourceforge.seqware.common.factory
 
BeanFactory() - Constructor for class net.sourceforge.seqware.common.factory.BeanFactory
 
BEDExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters
 
BEDExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.BEDExporter
 
BedFeatureImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
BedFeatureImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.BedFeatureImportWorker
 
benchmark() - Method in class com.github.seqware.queryengine.tutorial.Poster
 
benchmark() - Method in class com.github.seqware.queryengine.tutorial.PosterSGE
 
BENCHMARKING_BATCH_SIZE - Static variable in class com.github.seqware.queryengine.tutorial.Poster
 
BENCHMARKING_BATCH_SIZE - Static variable in class com.github.seqware.queryengine.tutorial.PosterSGE
 
BerkeleyDBFactory - Class in net.sourceforge.seqware.queryengine.backend.factory.impl
 
BerkeleyDBFactory() - Constructor for class net.sourceforge.seqware.queryengine.backend.factory.impl.BerkeleyDBFactory
 
BerkeleyDBStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl
 
BerkeleyDBStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
Bfast - Class in net.sourceforge.seqware.pipeline.modules.alignment
 
Bfast() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
 
biMap - Variable in class com.github.seqware.queryengine.impl.ProtobufSerialization
 
bind(HttpServletRequest, Object) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
bindSessionToThread() - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
 
bindSessionToThread(FlushMode) - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
 
binSize - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
BlobReaderWriter - Class in net.sourceforge.seqware.queryengine.prototypes
 
BlobReaderWriter() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.BlobReaderWriter
 
blockCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
blockSizes - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
blockStarts - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
bmfsplit - Class in net.sourceforge.seqware.pipeline.modules
 
bmfsplit() - Constructor for class net.sourceforge.seqware.pipeline.modules.bmfsplit
 
BrianTest - Class in com.github.seqware.queryengine.tutorial
This is a quick and sample application built on top of our API, created during the August 9th Hackathon.
BrianTest(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.BrianTest
 
brokerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
BufferedReaderThread - Class in net.sourceforge.seqware.common.util.iotools
 
BufferedReaderThread(InputStream) - Constructor for class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
 
BUFFERSIZE - Static variable in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
build() - Method in class com.github.seqware.queryengine.model.Analysis.Builder
 
build() - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
build() - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.Group.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
 
build() - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder
Build a Atom
build() - Method in class com.github.seqware.queryengine.model.Reference.Builder
 
build() - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
build() - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.User.Builder
 
Buildable<T extends BaseBuilder> - Interface in com.github.seqware.queryengine.model.interfaces
An interface for the various builders that we will use to construct models for managed objects
buildAnalysis() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a new analysis
buildAnalysis() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildAnalysisSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build an analysis set
buildAnalysisSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildDirectory(File) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil
 
buildFeature() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a feature
buildFeature() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildFeatureSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a featureSet with a reference
buildFeatureSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildFeatureSetInternal() - Method in class com.github.seqware.queryengine.impl.MRHBaseModelManager
 
buildFeatureSetInternal() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildGroup() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a group
buildGroup() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
buildReference() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a Reference with a given name
buildReference() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildReferenceSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a new reference set
buildReferenceSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildTag() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a Tag
buildTag() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildTagSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a set of tags
buildTagSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
buildUser() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a user
buildUser() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
BulkDownloaderController - Class in net.sourceforge.solexatools.webapp.controller
 
BulkDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
 
BulkDownloaderSizeValidatorController - Class in net.sourceforge.solexatools.webapp.controller
 
BulkDownloaderSizeValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController
 
BulkDownloadListController - Class in net.sourceforge.solexatools.webapp.controller
 
BulkDownloadListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
 
BulkDownloadListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
 
BulkDownloadListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
BulkProvisionFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module takes one or more inputs (S3 URL, HTTP/HTTPS URL, or local file path) and copies the file to the specified output (S3 bucket URL, HTTP/HTTPS URL, or local directory path).
BulkProvisionFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
 
BulkUtil - Class in net.sourceforge.solexatools.util
 
BulkUtil() - Constructor for class net.sourceforge.solexatools.util.BulkUtil
 
Bundle - Class in net.sourceforge.seqware.pipeline.bundle
This is a utility class that lets you manipulate a workflow bundle.
Bundle() - Constructor for class net.sourceforge.seqware.pipeline.bundle.Bundle
 
Bundle(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.bundle.Bundle
 
bundleDir - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
BundleInfo - Class in net.sourceforge.seqware.pipeline.bundle
 
BundleInfo() - Constructor for class net.sourceforge.seqware.pipeline.bundle.BundleInfo
 
BundleManager - Class in net.sourceforge.seqware.pipeline.plugins
 
BundleManager() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BundleManager
 
bundleUtil - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
BWA - Class in net.sourceforge.seqware.pipeline.modules.alignment
Align reads via BWA.
BWA() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.BWA
 
BWA_0_5_9 - Class in net.sourceforge.seqware.pipeline.modules.alignment.bwa
Align reads via BWA.
BWA_0_5_9() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
 
byte2HexString(byte[]) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisSetIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO
 
byteArr2m(byte[]) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
 
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO
 

C

CachedTagResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
CachedTagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CachedTagResource
 
calculateTotalTime(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
 
calledBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
calledBaseCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
calledBaseCountForward - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
calledBaseCountReverse - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
callOne - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
callTwo - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
CancelAnalysisWorkflowController - Class in net.sourceforge.solexatools.webapp.controller
 
CancelAnalysisWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
 
CancelBulkDownloaderController - Class in net.sourceforge.solexatools.webapp.controller
 
CancelBulkDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController
 
CancelInputDownloaderController - Class in net.sourceforge.solexatools.webapp.controller
 
CancelInputDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController
 
CASCADE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
causedBy(Throwable, Class) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
 
centerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
centername - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
centerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
centerprojectname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
cfg - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
ChangeNumberPopupPageController - Class in net.sourceforge.solexatools.webapp.controller
 
ChangeNumberPopupPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
 
ChangeWorkflowParamValueController - Class in net.sourceforge.solexatools.webapp.controller
 
ChangeWorkflowParamValueController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
 
CHECK - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
CHECK - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
checkCommandIO() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
checkCommandIO() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
checkExit(int) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
 
checkFileDetails(ReturnValue, FileMetadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Performs any additional checks on the file before adding it to the list of files to incorporate.
CheckForCycles - Class in net.sourceforge.seqware.common.hibernate
 
CheckForCycles() - Constructor for class net.sourceforge.seqware.common.hibernate.CheckForCycles
 
checkFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder
Check a row key
checkOutput(String) - Static method in class com.github.seqware.queryengine.system.Utility
Check whether we can create the output for a particular filename
checkPassword(String) - Method in class com.github.seqware.queryengine.model.User
Check a user's password
checkPermission(Permission) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
 
checkPermission(Permission, Object) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
 
checkpoint() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
checkProcessing(Processing) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles
 
checkSample(Sample) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles
 
checkStudy(Integer) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles
 
checksum - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
 
checksumMethod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
 
childMaps - Variable in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
childTags - Variable in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
clean_up() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
clean_up() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
clean_up() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
A cleanup method, make sure you cleanup files that are outside the current working directory since Pegasus won't clean those for you.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
A cleanup method, make sure you cleanup files that are outside the current working directory since Pegasus won't clean those for you.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
A cleanup method, make sure you cleanup files that are outside the current working directory since Pegasus won't clean those for you.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
A cleanup method, make sure you cleanup files that are outside the current working directory since Pegasus won't clean those for you.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
A cleanup method, make sure you cleanup files that are outside the current working directory since Pegasus won't clean those for you.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
Optional: Cleanup.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
A cleanup method, this cleans up the temporary file created.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
clean_up() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
 
cleanup() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
 
cleanup() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
cleanup() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clear() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Erase the current set of managed models without saving them to the back-end
clear() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
clearAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clearAnalysisIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clearDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clearFeatures() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
clearFeatures() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearFeatureSetIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clearGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clearGrps() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
clearPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearReferenceIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearRights() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clearRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearStorage() - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
clearStorage() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
clearStorage() - Method in class com.github.seqware.queryengine.impl.StorageInterface
For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStorage() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
clearStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearTags() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearTags() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearTagSpecIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clearTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clearUsers() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
cli2Map(String[], Map<String, String>) - Static method in class com.github.seqware.queryengine.common.MapTools
Method to getValues all "--key=value" or "--key value" parameters and add them to hashmap
cli2Map(String[], Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
Method to getValues all "--key=value" or "--key value" parameters and add them to hashmap
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clone(Processing) - Static method in class net.sourceforge.seqware.common.model.Processing
 
clone() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
clone() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.File
 
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.Processing
 
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.Registration
 
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.WorkflowRun
 
cloneToHibernate(Processing) - Static method in class net.sourceforge.seqware.common.model.Processing
 
cloneToHibernate(WorkflowRun) - Static method in class net.sourceforge.seqware.common.model.WorkflowRun
 
close() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Convenience method to flush() all entities and clear().
close() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
close() - Static method in class net.sourceforge.seqware.common.factory.DBAccess
 
close() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
close() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
 
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
 
close() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator
 
closeImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator
 
closeImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Closes the database iterator.
closeStorage() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Close the currently operating storage method
closeStorage() - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
closeStorage() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
closeStorage() - Method in class com.github.seqware.queryengine.impl.StorageInterface
Some storage types should be explicitly told when shutting down to release resources.
closeStorage() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
codingStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
codingStop - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
collectFlags - Class in net.sourceforge.seqware.pipeline.modules.qc
Collecting flag information per lane Underlying script: sw_module_extractFlag.pl Necessary programs: perl Expected output: flowcell.lane.flagCollection.txt
collectFlags() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
 
collectProcessingList(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource
 
color - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
 
colormatrix - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
colormatrixcode - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
com.github.seqware.queryengine - package com.github.seqware.queryengine
The base directory for the SeqWare Query Engine, we only have constants defined here for now.
com.github.seqware.queryengine.common - package com.github.seqware.queryengine.common
Contains copies of classes from seqware-common in the SVN SeqWare repo.
com.github.seqware.queryengine.dto - package com.github.seqware.queryengine.dto
 
com.github.seqware.queryengine.factory - package com.github.seqware.queryengine.factory
Provides the classes that the RESTful interface will use to construct interfaces that use the back-end without reference to the specific back-end.
com.github.seqware.queryengine.impl - package com.github.seqware.queryengine.impl
Provides the classes that implement the actual back-end for various database (or lack of database) types
com.github.seqware.queryengine.impl.protobufIO - package com.github.seqware.queryengine.impl.protobufIO
This package contains the classes that specifically handle protobuffer serialization to and from the back-end.
com.github.seqware.queryengine.impl.tuplebinderIO - package com.github.seqware.queryengine.impl.tuplebinderIO
This package contains the a couple of experimental classes that would have to be substantially added to in order to add BerkeleyDB serialization support.
com.github.seqware.queryengine.kernel - package com.github.seqware.queryengine.kernel
This package contains supporting classes for Queries.
com.github.seqware.queryengine.model - package com.github.seqware.queryengine.model
Provides the classes that the RESTful API will interact with.
com.github.seqware.queryengine.model.impl - package com.github.seqware.queryengine.model.impl
Provides the classes that implement model entities that the RESTful interface will interact with
com.github.seqware.queryengine.model.impl.hbasemrlazy - package com.github.seqware.queryengine.model.impl.hbasemrlazy
Provides classes that 'lazily' allow their members to persist their own membership and use Map/Reduce to determine attributes about themselves.
com.github.seqware.queryengine.model.impl.inMemory - package com.github.seqware.queryengine.model.impl.inMemory
Provides classes that support a simple in-memory implementation of the various model classes.
com.github.seqware.queryengine.model.impl.lazy - package com.github.seqware.queryengine.model.impl.lazy
Provides classes that 'lazily' allow their members to persist their own membership.
com.github.seqware.queryengine.model.interfaces - package com.github.seqware.queryengine.model.interfaces
 
com.github.seqware.queryengine.plugins - package com.github.seqware.queryengine.plugins
Provides the interfaces that an external plugin developer would need to conform to in order for the Query Engine to install and run properly.
com.github.seqware.queryengine.plugins.hbasemr - package com.github.seqware.queryengine.plugins.hbasemr
Provides classes that support and implement hbase implementations of plug-ins.
com.github.seqware.queryengine.plugins.inmemory - package com.github.seqware.queryengine.plugins.inmemory
Provides classes that support and implement in-memory mock-ups for plugins.
com.github.seqware.queryengine.plugins.lazyinmemory - package com.github.seqware.queryengine.plugins.lazyinmemory
Provides classes that support and implement in-memory mock-ups for plugins while being aware of lazy classes.
com.github.seqware.queryengine.system - package com.github.seqware.queryengine.system
 
com.github.seqware.queryengine.system.exporters - package com.github.seqware.queryengine.system.exporters
Command-line tools for exporting files to external file types.
com.github.seqware.queryengine.system.importers - package com.github.seqware.queryengine.system.importers
Command-line tools for importing files from external file types.
com.github.seqware.queryengine.system.importers.workers - package com.github.seqware.queryengine.system.importers.workers
Multi-threaded workers that handle the actual work for the FeatureImporter when exporting to various external file types.
com.github.seqware.queryengine.tutorial - package com.github.seqware.queryengine.tutorial
Classes for testing and hacking new tools.
com.github.seqware.queryengine.util - package com.github.seqware.queryengine.util
Provides utility classes for accessing this API via the model
com.github.seqware.queryengine.util.obo - package com.github.seqware.queryengine.util.obo
 
commaSeparateMy(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
commonname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
 
commonTimestamp - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
compare(ExperimentSpotDesignReadSpec, ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator
 
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.ContigPositionComparator
 
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.IntegerIdComparator
 
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.TagComparator
 
CompareDatabasesWithROC - Class in net.sourceforge.seqware.queryengine.examples
 
CompareDatabasesWithROC() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC
 
CompareDatabasesWithROCHBase - Class in net.sourceforge.seqware.queryengine.examples
 
CompareDatabasesWithROCHBase() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase
 
CompareDatabasesWithROCOld - Class in net.sourceforge.seqware.queryengine.examples
 
CompareDatabasesWithROCOld() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCOld
 
compareTo(SequencerRunReport.Row) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
compareTo(Expense) - Method in class net.sourceforge.seqware.common.model.Expense
 
compareTo(Experiment) - Method in class net.sourceforge.seqware.common.model.Experiment
 
compareTo(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
compareTo(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
compareTo(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
compareTo(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
compareTo(File) - Method in class net.sourceforge.seqware.common.model.File
 
compareTo(FileType) - Method in class net.sourceforge.seqware.common.model.FileType
 
compareTo(Invoice) - Method in class net.sourceforge.seqware.common.model.Invoice
 
compareTo(IUS) - Method in class net.sourceforge.seqware.common.model.IUS
 
compareTo(IUSAttribute) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
compareTo(Lane) - Method in class net.sourceforge.seqware.common.model.Lane
 
compareTo(LaneAttribute) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
compareTo(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
compareTo(LibrarySource) - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
compareTo(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
compareTo(Organism) - Method in class net.sourceforge.seqware.common.model.Organism
 
compareTo(Platform) - Method in class net.sourceforge.seqware.common.model.Platform
 
compareTo(Processing) - Method in class net.sourceforge.seqware.common.model.Processing
 
compareTo(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
compareTo(Registration) - Method in class net.sourceforge.seqware.common.model.Registration
 
compareTo(Sample) - Method in class net.sourceforge.seqware.common.model.Sample
 
compareTo(SampleAttribute) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
compareTo(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
compareTo(SequencerRunAttribute) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
compareTo(ShareStudy) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
compareTo(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
compareTo(Study) - Method in class net.sourceforge.seqware.common.model.Study
 
compareTo(StudyAttribute) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
compareTo(StudyType) - Method in class net.sourceforge.seqware.common.model.StudyType
 
compareTo(Workflow) - Method in class net.sourceforge.seqware.common.model.Workflow
 
compareTo(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
compareTo(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
compareTo(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
compareTo(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
compareTo(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
compareTo(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
compareTo(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
compareTo(StudySampleReportFileLineItem) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
compareTo(StudySampleReportLineItem) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
CompareTwoVariantAndCoverageDatabases - Class in net.sourceforge.seqware.queryengine.tools.reporters
 
CompareTwoVariantAndCoverageDatabases() - Constructor for class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantAndCoverageDatabases
 
CompareTwoVariantDatabases - Class in net.sourceforge.seqware.queryengine.tools.reporters
 
CompareTwoVariantDatabases() - Constructor for class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantDatabases
 
compareWorkflowRunFiles(String, List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Tests if the files from the workflow run (workflowRunAcc) are the same as those found in the database (filesToRun).
COMPLETED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
 
Compress - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module extends allows for compressing and decompressing files.
Compress() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.Compress
 
compressed - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
COMPRESSED_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
Compression - Class in com.github.seqware.queryengine.kernel
Static methods for compressing/decompressing user data.
Compression() - Constructor for class com.github.seqware.queryengine.kernel.Compression
 
config - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
config - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
config - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
config - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
config - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
ConfigTools - Class in com.github.seqware.queryengine.common
 
ConfigTools() - Constructor for class com.github.seqware.queryengine.common.ConfigTools
 
ConfigTools - Class in net.sourceforge.seqware.common.util.configtools
 
ConfigTools() - Constructor for class net.sourceforge.seqware.common.util.configtools.ConfigTools
 
configureHBaseConfig(Configuration) - Static method in class com.github.seqware.queryengine.impl.HBaseStorage
Configure a HBaseConfiguration with a given set of properties
consensusAveSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
consensusBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
consensusCallQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
consensusMaxSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
Consequence - Class in net.sourceforge.seqware.queryengine.backend.model
 
Consequence() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
CONSEQUENCE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
ConsequenceResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
ConsequenceResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.ConsequenceResource
 
ConsequenceTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
ConsequenceTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
 
ConsequenceVariantIdKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
 
ConsequenceVariantIdKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ConsequenceVariantIdKeyCreator
 
consolidateRow(List<FeatureList>) - Static method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Given a collection of FeatureLists all with the same row key (and differing timestamps), create a consistent view of the features in the feature set corresponding effectively to the last timestamp
CONST_AT_SIGN - Static variable in class net.sourceforge.solexatools.validation.LoginValidator
 
Constant - Class in net.sourceforge.solexatools.util
 
Constant() - Constructor for class net.sourceforge.solexatools.util.Constant
 
Constants - Class in com.github.seqware.queryengine
Defaults for our Constants are defined here and can be overridden by entries in the ~/.seqware/settings file.
Constants() - Constructor for class com.github.seqware.queryengine.Constants
 
Constants.Term - Enum in com.github.seqware.queryengine
 
contact - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS
 
contacts - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
containsKey(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
containsKey(String) - Method in interface com.github.seqware.queryengine.model.TagSet
 
ContextImpl - Class in net.sourceforge.seqware.common
 
contig - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
contig - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
ContigPosition - Class in net.sourceforge.seqware.queryengine.backend.model
 
ContigPosition() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
 
CONTIGPOSITION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
ContigPositionComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
 
ContigPositionComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.ContigPositionComparator
 
ContigPositionKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
 
ContigPositionKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ContigPositionKeyCreator
 
ContigPositionTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
ContigPositionTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
 
ControllerUtil - Class in net.sourceforge.solexatools.util
 
ControllerUtil() - Constructor for class net.sourceforge.solexatools.util.ControllerUtil
 
ConvertBAMTranscript2Genome - Class in net.sourceforge.seqware.pipeline.modules.BamFilters
Translate reads mapped to transcripts to genomic coordinates.
ConvertBAMTranscript2Genome() - Constructor for class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
 
copy(boolean) - Method in interface com.github.seqware.queryengine.model.Atom
Copy constructor, used to generate a shallow copy of a Atom ith potentially a new timestamp and UUID
copy(boolean) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Copy constructor, used to generate a shallow copy of a Atom with potentially a new clientTimestamp and UUID
copyBundle(String, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
copyBundleToS3(File, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
copyInputStream(InputStream, OutputStream) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
copyInputStream(InputStream, OutputStream) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil
 
copyProperty(Object, String, Object) - Method in class net.sourceforge.seqware.common.util.NullBeanUtils
 
copyToFile(BufferedInputStream, String, int, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Copy reader into output.
copyToFile(BufferedInputStream, String, int, String, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Copy reader into output using Cipher.
count - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
countOfRows(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService
 
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService
 
countOfRows(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
countOfRows(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
 
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
 
countOfRows(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
countOfStatus(Study, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
countOfStatus(SequencerRun, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
countOfStatus(Study, Workflow, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
countOfStatus(SequencerRun, Workflow, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
countOfStatus(Study, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
countOfStatus(Study, Workflow, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
countOfStatus(SequencerRun, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
countOfStatus(SequencerRun, Workflow, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
countOfStatus(Study, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
countOfStatus(Study, Workflow, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
countOfStatus(SequencerRun, Workflow, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
countOfStatus(SequencerRun, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
countOfStatus(Study, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
countOfStatus(SequencerRun, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
countOfStatus(Study, Workflow, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
countOfStatus(SequencerRun, Workflow, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
Coverage - Class in net.sourceforge.seqware.queryengine.backend.model
 
Coverage() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
coverage - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
COVERAGE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
CoverageIteratorProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators
 
CoverageIteratorProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.CoverageIteratorProcessor
 
CoverageProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
 
CoverageProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
CoverageResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
CoverageResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CoverageResource
 
CoveragesResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
CoveragesResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CoveragesResource
 
CoverageStatsProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
 
CoverageStatsProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor
 
CoverageTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
CoverageTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
 
coverageXTranscript - Class in net.sourceforge.seqware.pipeline.modules.qc
To get coverage across transcript plot Underlying script: sw_module_CoverageAcrossTranscript.pl (by Sara Grimm) Necessary programs: perl, path to samtools Input: alignment file (bam) a map file, which is generated by the PrepTranscriptDB module, currently, ~/svnroot/seqware-complete/trunk/seqware-pipeline/data/annotation_reference/hg19_transcripts.hg19.20091027.trmap Expected output: coverage across transcript plot
coverageXTranscript() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
 
create(SampleSearch) - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
 
create(SampleSearch) - Method in interface net.sourceforge.seqware.common.business.SampleSearchService
 
create(SampleSearch) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
 
create(SampleSearch) - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO
 
create() - Static method in class net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator
 
createANALYSIS(AnalysisType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<AnalysisType>}
createANALYSISSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisSet
createAnalysisType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType
createAnalysisTypeANALYSISATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISATTRIBUTES
createAnalysisTypeANALYSISATTRIBUTESANALYSISATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
createAnalysisTypeANALYSISFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISFILES
createAnalysisTypeANALYSISFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISFILES.FILE
createAnalysisTypeANALYSISLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS
createAnalysisTypeANALYSISLINKSANALYSISLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKXREFLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
createAnalysisTypeANALYSISTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISTYPE
createAnalysisTypePARENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT
createAnalysisTypePARENTEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.EXPERIMENTREF
createAnalysisTypePARENTRUNREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.RUNREF
createAnalysisTypePARENTSAMPLEPOOLREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.SAMPLEPOOLREF
createAnalysisTypePARENTSAMPLEPOOLREFMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
createAnalysisTypePARENTSAMPLEREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.SAMPLEREF
createAnalysisTypePARENTSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.STUDYREF
createDatabase() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
 
createDatabase() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
 
createDirectoryWithUniqueName(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
createEXPERIMENT(ExperimentType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<ExperimentType>}
createEXPERIMENTSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentSet
createExperimentType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType
createExperimentTypeDESIGN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN
createExperimentTypeDESIGNLIBRARYDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR
createExperimentTypeDESIGNLIBRARYDESCRIPTORLIBRARYLAYOUT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
createExperimentTypeDESIGNLIBRARYDESCRIPTORLIBRARYLAYOUTPAIRED() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
createExperimentTypeDESIGNSAMPLEDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.SAMPLEDESCRIPTOR
createExperimentTypeDESIGNSPOTDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR
createExperimentTypeDESIGNSPOTDESCRIPTORSPOTDECODESPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
createExperimentTypeDESIGNSPOTDESCRIPTORSPOTDECODESPECREADSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
createExperimentTypeEXPERIMENTATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTATTRIBUTES
createExperimentTypeEXPERIMENTATTRIBUTESEXPERIMENTATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
createExperimentTypeEXPERIMENTLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTLINKS
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
createExperimentTypePLATFORM() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM
createExperimentTypePLATFORMABISOLID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.ABISOLID
createExperimentTypePLATFORMABISOLIDCOLORMATRIX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
createExperimentTypePLATFORMABISOLIDCOLORMATRIXCOLOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
createExperimentTypePLATFORMHELICOS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.HELICOS
createExperimentTypePLATFORMILLUMINA() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.ILLUMINA
createExperimentTypePLATFORMLS454() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.LS454
createExperimentTypePROCESSING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PROCESSING
createExperimentTypePROCESSINGBASECALLS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PROCESSING.BASECALLS
createExperimentTypePROCESSINGQUALITYSCORES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PROCESSING.QUALITYSCORES
createExperimentTypeSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.STUDYREF
createFileWithUniqueName(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
createInboundRoot() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
Creates a root Restlet that will receive all incoming calls.
createInboundRoot() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
Creates a root Restlet that will receive all incoming calls.
createINI(HashMap<String, String>) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
 
createJavaJob(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createJob(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createKey(Atom) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
createKey(SGID) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
createKey(SGID, boolean) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
createPreJobDirtory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
createRUN(RunType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<RunType>}
createRUNSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunSet
createRunType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType
createRunTypeDATABLOCK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.DATABLOCK
createRunTypeDATABLOCKFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.DATABLOCK.FILES
createRunTypeDATABLOCKFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.DATABLOCK.FILES.FILE
createRunTypeEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.EXPERIMENTREF
createRunTypeRUNATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNATTRIBUTES
createRunTypeRUNATTRIBUTESRUNATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNATTRIBUTES.RUNATTRIBUTE
createRunTypeRUNLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNLINKS
createRunTypeRUNLINKSRUNLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNLINKS.RUNLINK
createRunTypeRUNLINKSRUNLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNLINKS.RUNLINK.ENTREZLINK
createRunTypeRUNLINKSRUNLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNLINKS.RUNLINK.URLLINK
createSAMPLE(SampleType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<SampleType>}
createSAMPLESET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleSet
createSampleType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType
createSampleTypeMEMBERS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.MEMBERS
createSampleTypeMEMBERSMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.MEMBERS.MEMBER
createSampleTypeSAMPLEATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLEATTRIBUTES
createSampleTypeSAMPLEATTRIBUTESSAMPLEATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
createSampleTypeSAMPLELINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLELINKS
createSampleTypeSAMPLELINKSSAMPLELINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLELINKS.SAMPLELINK
createSampleTypeSAMPLELINKSSAMPLELINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
createSampleTypeSAMPLELINKSSAMPLELINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
createSampleTypeSAMPLENAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLENAME
createSecondaryKey(SecondaryDatabase, DatabaseEntry, DatabaseEntry, DatabaseEntry) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ConsequenceVariantIdKeyCreator
 
createSecondaryKey(SecondaryDatabase, DatabaseEntry, DatabaseEntry, DatabaseEntry) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ContigPositionKeyCreator
 
createSecondaryKeys(SecondaryDatabase, DatabaseEntry, DatabaseEntry, Set) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyCreator
 
createSecondaryKeys(SecondaryDatabase, DatabaseEntry, DatabaseEntry, Set) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyOnlyCreator
 
createSeqwareModuleJob(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createSeqwareModuleJob(String, boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createSeqwareModuleJob(String, Module) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createSeqwareModuleJob(String, Module, boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createSTUDY(StudyType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<StudyType>}
createSTUDYSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudySet
createStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType
createStudyTypeDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.DESCRIPTOR
createStudyTypeDESCRIPTORSTUDYABSTRACT(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<String>}
createStudyTypeDESCRIPTORSTUDYTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.DESCRIPTOR.STUDYTYPE
createStudyTypeSTUDYATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYATTRIBUTES
createStudyTypeSTUDYATTRIBUTESSTUDYATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
createStudyTypeSTUDYLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYLINKS
createStudyTypeSTUDYLINKSSTUDYLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYLINKS.STUDYLINK
createStudyTypeSTUDYLINKSSTUDYLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
createStudyTypeSTUDYLINKSSTUDYLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYLINKS.STUDYLINK.URLLINK
createSUBMISSION(SubmissionType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<SubmissionType>}
createSUBMISSIONSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionSet
createSubmissionType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType
createSubmissionTypeACTIONS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS
createSubmissionTypeACTIONSACTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION
createSubmissionTypeACTIONSACTIONADD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.ADD
createSubmissionTypeACTIONSACTIONHOLD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.HOLD
createSubmissionTypeACTIONSACTIONMODIFY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.MODIFY
createSubmissionTypeACTIONSACTIONRELEASE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.RELEASE
createSubmissionTypeACTIONSACTIONSUPPRESS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.SUPPRESS
createSubmissionTypeACTIONSACTIONVALIDATE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.VALIDATE
createSubmissionTypeCONTACTS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.CONTACTS
createSubmissionTypeCONTACTSCONTACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.CONTACTS.CONTACT
createSubmissionTypeFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.FILES
createSubmissionTypeFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.FILES.FILE
createSubmittableJob(Configuration, String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest
Sets up the actual job.
createSubmittableJob(Configuration, String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2
Sets up the actual job.
createSymlink(String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Creates symlink of input to output.
createTargetDirectory(String, String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Creates abstract pathname.
createTargetPath(String, String, String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Creates abstract pathname.
createTempDirectory(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
CreateUpdateManager - Interface in com.github.seqware.queryengine.factory
A very simple Manager that is somewhat like a very stripped down EntityManager from JPA allowing us to create Models and persist them, in other words this handles Create and Update operations out of the basic CRUD operations.
CreateUpdateManager.State - Enum in com.github.seqware.queryengine.factory
This manager defines Atoms to be in the following states
CreateVariantDB - Class in net.sourceforge.seqware.pipeline.modules.queryengine
Purpose: This module serves to create a variant database from the SeqWare Query Engine project that contains SNVs, small indels, and coverage.
CreateVariantDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
CSV_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
CSV_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
currGenomeTagIndexTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
currStep - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
currStep - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
CursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
 
CursorIterator(Cursor, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
 
CustomIntegerEditor - Class in net.sourceforge.solexatools.validation
 
CustomIntegerEditor() - Constructor for class net.sourceforge.solexatools.validation.CustomIntegerEditor
 
CycleChecker - Class in net.sourceforge.seqware.pipeline.plugins
 
CycleChecker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.CycleChecker
 
CycleCheckResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
CycleCheckResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource
 
cyclecoord - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
cyclecount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
cyclecount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
 
cyclesequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
 

D

data - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
DatabaseCreator - Class in net.sourceforge.seqware.common.util.testtools
 
DatabaseCreator() - Constructor for class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
 
DatabaseIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
DatabaseIDResource(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
 
DatabaseResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
DatabaseResource(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.DatabaseResource
 
datablock - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
dataDecryptionKey - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
dataEncryptionKey - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
dataEncryptionKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
dataSource() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig
 
DATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
DATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
Daxgenerator - Class in net.sourceforge.seqware.pipeline.daxgenerator
 
Daxgenerator() - Constructor for class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
 
DaxgeneratorV2 - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus
 
DaxgeneratorV2() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.DaxgeneratorV2
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
 
DB_CONN_STRING - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DB_NAME - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DB_PASS - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DB_SERVER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DB_USER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DBAccess - Class in net.sourceforge.seqware.common.factory
 
DBCOULDNOTDISCONNECT - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
DBCOULDNOTINITIALIZE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
debug(Object) - Static method in class com.github.seqware.queryengine.common.Log
See Category.debug(Object).
debug(Object, Throwable) - Static method in class com.github.seqware.queryengine.common.Log
See Category.debug(Object,Throwable).
DEBUG - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage
 
debug(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.debug(Object).
debug(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.debug(Object,Throwable).
debug - Variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
 
Debug - Class in net.sourceforge.solexatools
 
Debug() - Constructor for class net.sourceforge.solexatools.Debug
 
Decider - Class in net.sourceforge.seqware.pipeline.decider
 
Decider() - Constructor for class net.sourceforge.seqware.pipeline.decider.Decider
Notes: Things I would like taken care of for me: * all params in a hash (from both DB and ini file provided) * a list of hashmap that represent a filtered list of files by sample, study, experiment, workflow, etc * a list of files that represent the output from this workflow * a hash that joins the output of this workflow to their parents * the master list of results should be configurable, either to have all the processing events removed where this workflow has already been run or to include these
DeciderInterface - Interface in net.sourceforge.seqware.pipeline.decider
 
DefaultConfig - Class in net.sourceforge.seqware.pipeline.runner
Default Configuation class.
DefaultConfig() - Constructor for class net.sourceforge.seqware.pipeline.runner.DefaultConfig
 
delete(Experiment, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
delete(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
 
delete(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
 
delete(File, String) - Method in interface net.sourceforge.seqware.common.business.FileService
 
delete(Experiment, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
delete(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
 
delete(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
 
delete(File, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
delete(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
delete(IUS, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
delete(Lane, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Deletes an instance of Lane in the database.
delete(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
delete(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
delete(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
delete(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
delete(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
delete(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
delete(Processing, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
delete(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
delete(Sample, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Deletes an instance of Sample in the database.
delete(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Deletes an instance of SequencerRun in the database.
delete(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
delete(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
delete(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
delete(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
delete(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
delete(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
 
delete(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
 
delete(Study, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Updates an instance of Study in the database.
delete(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
delete(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
delete(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
delete(WorkflowRun, String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
delete(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
delete(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
delete(IUS, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
delete(Lane, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
delete(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
 
delete(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
 
delete(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
 
delete(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
 
delete(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
 
delete(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
 
delete(Processing, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
delete(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
 
delete(Sample, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
delete(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
delete(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
delete(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
delete(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
delete(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
delete(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
delete(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
delete(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
delete(Study, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
delete(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
delete(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
delete(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
delete(WorkflowRun, String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
delete(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
delete(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
 
delete(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
delete(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
 
delete(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
 
delete(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
 
delete(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
delete(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
 
delete(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
delete(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
 
delete(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
 
delete(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
 
delete(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
Updates an instance of File in the database.
delete(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
delete(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
 
delete(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
delete(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO
 
delete(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
 
delete(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
 
delete(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
 
delete(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
Deletes an instance of Lane in the database.
delete(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
delete(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
 
delete(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
 
delete(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
 
delete(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
Updates an instance of Processing in the database.
delete(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
 
delete(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
 
delete(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
 
delete(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
delete(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
 
delete(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
 
delete(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
 
delete(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
 
delete(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
Deletes an instance of Sample in the database.
delete(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
 
delete(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
delete(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
delete(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
delete(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
delete(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
delete(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
delete(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
Updates an instance of ShareStudy in the database.
delete(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
Updates an instance of ShareWorkflowRun in the database.
delete(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
 
delete(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
delete(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
 
delete(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
 
delete(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
delete(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
delete(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
delete(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
 
delete(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
delete(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
delete(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
delete(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
 
delete(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
delete(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
delete(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
delete(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
 
delete(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
delete(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
 
delete(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
 
delete(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
 
delete(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
 
delete(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
 
delete(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
 
delete(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
 
delete(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
 
delete(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
delete(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
 
delete(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
delete(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
 
delete(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
 
delete(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
 
delete(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
 
delete(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
 
delete(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
 
delete(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
delete(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
 
delete(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
delete(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
 
delete(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
 
delete(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
delete(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
 
delete(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
 
delete(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
 
delete(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
delete(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
delete() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
 
delete() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
 
delete() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
 
deleteAll(List<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService
 
deleteAll(List<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
deleteAll(List<File>) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
deleteAll(List<File>) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
deleteAllWithFolderStore(List<File>) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
deleteAllWithFolderStore(List<File>) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
deleteAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
 
deleteAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
 
deleteDirectoryRecursive(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
DeleteLoadedIndexPageController - Class in net.sourceforge.solexatools.webapp.controller
 
DeleteLoadedIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
 
DeleteTempFile(Registration) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
 
DELETION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
denovoassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
describeInterfaceAndImplementation(Object, String) - Static method in class net.sourceforge.solexatools.Debug
 
description - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
description - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
description - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
descriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.ApacheSerialization
 
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.KryoSerialization
 
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization
 
deserialize(byte[], Class<T>) - Method in interface com.github.seqware.queryengine.impl.SerializationInterface
Given an array of bytes, get back an atom
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.StorageInterface
Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.StorageInterface
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.StorageInterface
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.StorageInterface
Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.StorageInterface
Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
design - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
designdescription - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
destSet - Variable in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper
the feature set that we will be writing to, may be null
dibase - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
 
directBIMap - Variable in class com.github.seqware.queryengine.impl.StorageInterface
These tables are always created with the same names
DIRECTORYNOTREADABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
DIRECTORYNOTWRITABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
dirPathExistsAndReadable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
dirPathExistsAndWritable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
dissociateTag(Tag) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
dissociateTag(Tag) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Remove a new tag from a subject
dissociateTag(Tag) - Method in class com.github.seqware.queryengine.model.Tag
Tags are not taggable, but it is actually easier to have the capability via inheritance and just turn it off
do_run() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
 
do_run() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
do_run() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
do_run() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Performs the main tasks for the module.
do_run() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
This is the core of a module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
This is the core of a module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
This is the core of a module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
This is the core of a module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.Picard
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
Run core of module.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
The SNVMix and filter if specified are combined here.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
do_run() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
 
do_summary() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Just returns a summary of what would be run.
do_summary() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
do_test() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
 
do_test() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
do_test() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
do_test() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
This is really an optional method but a very good idea.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
This is really an optional method but a very good idea.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
This is really an optional method but a very good idea.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
This is really an optional method but a very good idea.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
This is really an optional method but a very good idea.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.Picard
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC
Things to check: *
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
Optional: Test program on a known data set.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
Optional: Test program on a known data set.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc
Things to check: *
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
Optional: Test program on a known data set.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
Optional: Test program on a known data set.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
Optional: Test program on a known data set.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
Optional: Test program on a known dataset.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
Things to check: *
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
Things to check: *
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
Things to check: *
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
Things to check: *
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
Not implemented.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
Things to check: * FIXME
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress
Things to check: * FIXME
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
Things to check: * FIXME
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
Things to check: * FIXME
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
Not implemented
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
Not implemented
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
Not implemented
do_test() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
do_verify_input() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Input data validation code goes here.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
The do_verify_input method ensures that the input files exist.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
The do_verify_input method ensures that the input files exist.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
The do_verify_input method ensures that the input is reasonable and valid for this tool.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
The do_verify_input method ensures that the input is reasonable and valid for this tool.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
The do_verify_input method ensures that the input files exist.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.Picard
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
Verify anything needed to run the module is ready (e.g.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
The do_verify_input method ensures that the model files exist.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
do_verify_output() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Perform post-task tests here.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
A method to check to make sure the output was created correctly
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
A method to check to make sure the output was created correctly
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
A method to check to make sure the output was created correctly
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
A method to check to make sure the output was created correctly
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
A method to check to make sure the output was created correctly
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.Picard
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
Check to make sure the output was created correctly.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
A method to check to make sure the output was created correctly
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
do_verify_parameters() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Parameter validation code goes here.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
Verifies that the parameters make sense
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
Verifies that the parameters make sense
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
Verifies that the parameters make sense
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
Verifies that the parameters make sense
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
Verifies that the required parameters are present
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.Picard
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
Verify that the parameters are defined & make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
Verifies that the parameters make sense.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
Just makes sure the param was passed in.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
Just makes sure the param was passed in.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
Just makes sure the param was passed in.
doCreateTableJson(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.BasicResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
 
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
 
doRetrieveListElements(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
doRun() - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect
 
doRun() - Method in class net.sourceforge.seqware.pipeline.runner.RedirectAspect
 
doSetupReport(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
 
DownloaderController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
DownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DownloaderController
 
DownloadFileListController - Class in net.sourceforge.solexatools.webapp.controller
 
DownloadFileListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
dqc - Class in net.sourceforge.seqware.pipeline.modules.qc
Purpose: This module generates pre and post alignment QC reports using dqc from the DNAA package.
dqc() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.dqc
 
dropDatabase() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
 
dropDatabase() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
 
Dtos - Class in net.sourceforge.seqware.webservice.dto
Methods to convert between domain objects and dtos.
Dtos() - Constructor for class net.sourceforge.seqware.webservice.dto.Dtos
 
DumpVariantDB - Class in net.sourceforge.seqware.pipeline.modules.queryengine
Purpose: This module takes a BerkeleyDB SeqWare Query Engine database and dumps the variants as a series of BED files, one per contig.
DumpVariantDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
dumpVCFFromFeatureSetID(FeatureSet, String) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper
 

E

echo - Class in net.sourceforge.seqware.pipeline.modules.examples
 
echo() - Constructor for class net.sourceforge.seqware.pipeline.modules.examples.echo
 
EMAILADDRESS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
END_ALL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
END_PMC_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
END_QUAL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
EntityController - Class in net.sourceforge.solexatools.webapp.controller
The controller.
EntityController() - Constructor for class net.sourceforge.solexatools.webapp.controller.EntityController
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
 
entryToObject(TupleInput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
 
entryToObject(TupleInput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
 
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
 
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
 
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
 
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
 
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
 
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
 
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
 
EnvUtil - Class in net.sourceforge.seqware.queryengine.webservice.util
 
EnvUtil() - Constructor for class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil
 
ENVVARNOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
equals(Object) - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
equals(Object) - Method in class com.github.seqware.queryengine.model.Feature
 
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.FeatureList
 
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
Override the equals method for Group, kind of a cheat With other objects we take into account things like version or SGID However, with Group, the object is embedded inside the ACL for other objects explicitly, so the version changes too often for easy API use
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
equals(Object) - Method in class com.github.seqware.queryengine.model.Tag
 
equals(Object) - Method in class com.github.seqware.queryengine.model.User
 
equals(Object) - Method in class com.github.seqware.queryengine.util.LazyReference
 
equals(Object) - Method in class com.github.seqware.queryengine.util.SGID
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Expense
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Experiment
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.File
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.FileType
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Invoice
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.IUS
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Lane
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Organism
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Platform
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Processing
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Project
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Registration
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Sample
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Study
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.StudyType
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.Workflow
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
 
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
error(Object) - Static method in class com.github.seqware.queryengine.common.Log
See Category.error(Object).
error(Object, Throwable) - Static method in class com.github.seqware.queryengine.common.Log
See Category.error(Object,Throwable).
error(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.error(Object).
error(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.error(Object,Throwable).
evaluate() - Method in class com.github.seqware.queryengine.kernel.RPNStack
RPN evaluation.
evaluateReturn(Module, String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner
 
evict(Object) - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
 
ExceptionTools - Class in net.sourceforge.seqware.common.util.exceptiontools
 
ExceptionTools() - Constructor for class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
 
executeQuery(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
executeUpdate(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
existingStudyType - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
 
existsExperiment(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsIUS(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsLane(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsProcessing(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsSample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsSequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
EXIT_CODE_EXISTING_NAME - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter
 
EXIT_CODE_INVALID_ARGS - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter
 
EXIT_CODE_INVALID_FILE - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter
 
ExitException - Exception in net.sourceforge.seqware.common.util
Created by IntelliJ IDEA.
ExitException(int) - Constructor for exception net.sourceforge.seqware.common.util.ExitException
 
exitStatus - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
ExonCountsRPKM - Class in net.sourceforge.seqware.pipeline.modules.quantification
Calculate base counts, coverage, & RPKM per exon given a BAM file of aligned reads and a list of exons.
ExonCountsRPKM() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
 
expectedbasecall - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
expectedNumberReads - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
expectedNumberRuns - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
expectedNumberSpots - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
Expense - Class in net.sourceforge.seqware.common.model
 
Expense() - Constructor for class net.sourceforge.seqware.common.model.Expense
 
EXPENSIVE_ITERATION_WARNED - Static variable in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Trigger a warning about iteration being expensive only once
Experiment - Class in net.sourceforge.seqware.common.model
 
Experiment() - Constructor for class net.sourceforge.seqware.common.model.Experiment
 
experiment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet
 
EXPERIMENT_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
EXPERIMENT_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
EXPERIMENT_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
 
EXPERIMENT_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
EXPERIMENT_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
ExperimentAttribute - Class in net.sourceforge.seqware.common.model
ExperimentAttribute generated by hbm2java
ExperimentAttribute() - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute
 
ExperimentAttribute(int, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute
 
ExperimentAttribute(int, Experiment, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute
 
experimentattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES
 
ExperimentAttributeDAO - Interface in net.sourceforge.seqware.common.dao
 
ExperimentAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ExperimentAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
 
experimentattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
ExperimentController - Class in net.sourceforge.solexatools.webapp.controller
ExperimentController
ExperimentController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
ExperimentController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
ExperimentDAO - Interface in net.sourceforge.seqware.common.dao
 
ExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
ExperimentIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
 
ExperimentIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
 
ExperimentIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
ExperimentIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
 
ExperimentLibraryDesign - Class in net.sourceforge.seqware.common.model
 
ExperimentLibraryDesign() - Constructor for class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
ExperimentLibraryDesignDAO - Interface in net.sourceforge.seqware.common.dao
 
ExperimentLibraryDesignDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ExperimentLibraryDesignDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
 
ExperimentLibraryDesignService - Interface in net.sourceforge.seqware.common.business
 
ExperimentLibraryDesignServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ExperimentLibraryDesignServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
 
ExperimentLink - Class in net.sourceforge.seqware.common.model
ExperimentLink generated by hbm2java
ExperimentLink() - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink
 
ExperimentLink(int, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink
 
ExperimentLink(int, Experiment, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink
 
experimentlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS
 
ExperimentLinkDAO - Interface in net.sourceforge.seqware.common.dao
 
ExperimentLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ExperimentLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
 
experimentlinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
ExperimentList - Class in net.sourceforge.seqware.common.model.lists
 
ExperimentList() - Constructor for class net.sourceforge.seqware.common.model.lists.ExperimentList
 
experimentref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
experimentref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
ExperimentResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
ExperimentResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
 
ExperimentService - Interface in net.sourceforge.seqware.common.business
 
ExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
ExperimentSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet
 
ExperimentSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
ExperimentSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
ExperimentSpotDesign - Class in net.sourceforge.seqware.common.model
 
ExperimentSpotDesign() - Constructor for class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
ExperimentSpotDesignDAO - Interface in net.sourceforge.seqware.common.dao
 
ExperimentSpotDesignDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ExperimentSpotDesignDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
 
ExperimentSpotDesignReadSpec - Class in net.sourceforge.seqware.common.model
 
ExperimentSpotDesignReadSpec() - Constructor for class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
ExperimentSpotDesignReadSpecComparator - Class in net.sourceforge.seqware.common.model.comparator
 
ExperimentSpotDesignReadSpecComparator() - Constructor for class net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator
 
ExperimentSpotDesignReadSpecDAO - Interface in net.sourceforge.seqware.common.dao
 
ExperimentSpotDesignReadSpecDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ExperimentSpotDesignReadSpecDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
 
ExperimentSpotDesignReadSpecService - Interface in net.sourceforge.seqware.common.business
 
ExperimentSpotDesignReadSpecServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ExperimentSpotDesignReadSpecServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
 
ExperimentSpotDesignService - Interface in net.sourceforge.seqware.common.business
 
ExperimentSpotDesignServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ExperimentSpotDesignServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
 
ExperimentType - Class in net.sourceforge.seqware.queryengine.webservice.model
An Experiment specifies of what will be sequenced and how the sequencing will be performed.
ExperimentType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
ExperimentType.DESIGN - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
ExperimentType.DESIGN.LIBRARYDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
 
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
 
ExperimentType.DESIGN.SAMPLEDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.SAMPLEDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
 
ExperimentType.DESIGN.SPOTDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
 
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
 
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
ExperimentType.EXPERIMENTATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES
 
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
 
ExperimentType.EXPERIMENTLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS
 
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
 
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
 
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
 
ExperimentType.PLATFORM - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
ExperimentType.PLATFORM.ABISOLID - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
 
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
 
ExperimentType.PLATFORM.HELICOS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.HELICOS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
 
ExperimentType.PLATFORM.ILLUMINA - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.ILLUMINA() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
 
ExperimentType.PLATFORM.LS454 - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.LS454() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
 
ExperimentType.PROCESSING - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PROCESSING() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
 
ExperimentType.PROCESSING.BASECALLS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PROCESSING.BASECALLS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
 
ExperimentType.PROCESSING.QUALITYSCORES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PROCESSING.QUALITYSCORES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
ExperimentType.STUDYREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.STUDYREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
 
ExperimentUpdateValidator - Class in net.sourceforge.solexatools.validation
 
ExperimentUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.ExperimentUpdateValidator
 
ExperimentValidator - Class in net.sourceforge.solexatools.validation
 
ExperimentValidator() - Constructor for class net.sourceforge.solexatools.validation.ExperimentValidator
 
EXPIRYTIME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
export() - Method in class com.github.seqware.queryengine.system.exporters.VCFDumper
 
export() - Method in class com.github.seqware.queryengine.tutorial.BrianTest
 
export() - Method in class com.github.seqware.queryengine.tutorial.GITest
 
EXT_PARAMETERS - Static variable in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
ext_parameters - Variable in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper
parameters that will be usable by the user (the writer of the queries)

F

Factory - Class in net.sourceforge.seqware.queryengine.backend.factory
 
Factory() - Constructor for class net.sourceforge.seqware.queryengine.backend.factory.Factory
 
FactoryInterface - Interface in net.sourceforge.seqware.queryengine.backend.factory
 
FAILED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
 
FAILED - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun
 
FAILED - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
FAILED - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
FAILURE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
Fastq(File, String, String, int) - Static method in class net.sourceforge.seqware.common.util.filetools.validate.Validate
 
fastqConvNum - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
fatal(Object) - Static method in class com.github.seqware.queryengine.common.Log
See Category.fatal(Object).
fatal(Object, Throwable) - Static method in class com.github.seqware.queryengine.common.Log
See Category.fatal(Object,Throwable).
fatal(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.fatal(Object).
fatal(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.fatal(Object,Throwable).
Feature - Class in com.github.seqware.queryengine.model
Features represent a GVF (which is a more generic version of a VCF).
Feature - Class in net.sourceforge.seqware.queryengine.backend.model
 
Feature() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Feature
 
feature - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
FEATURE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
Feature.AdditionalAttributeType - Enum in com.github.seqware.queryengine.model
 
Feature.Builder - Class in com.github.seqware.queryengine.model
 
Feature.Builder() - Constructor for class com.github.seqware.queryengine.model.Feature.Builder
 
Feature.Strand - Enum in com.github.seqware.queryengine.model
Strand locations of features.
FEATURE_SET_ID - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter
 
FEATURE_SET_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
 
FEATURE_SET_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
FeatureFilter - Interface in com.github.seqware.queryengine.plugins.inmemory
Interface for matching functions that we can quickly use in both in-memory and M/R plug-ins.
FeatureImporter - Class in com.github.seqware.queryengine.system.importers
Port of the class from the original prototype, adapted to use the new classes in the new API; command-line interface is the older one without support for SO.
FeatureImporter(int) - Constructor for class com.github.seqware.queryengine.system.importers.FeatureImporter
 
FeatureImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
 
FeatureImporter(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.FeatureImporter
 
FeatureIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
FeatureIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
 
FeatureList - Class in com.github.seqware.queryengine.model.impl
This is an internal atom class, that should never be viewed by the user.
FeatureList() - Constructor for class com.github.seqware.queryengine.model.impl.FeatureList
 
FeatureList.Builder - Class in com.github.seqware.queryengine.model.impl
 
FeatureList.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.FeatureList.Builder
 
FeatureListIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
FeatureListIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
 
featureNotImplemented() - Static method in class net.sourceforge.seqware.common.module.ReturnValue
 
featurePasses(Feature, Object...) - Method in interface com.github.seqware.queryengine.plugins.inmemory.FeatureFilter
 
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesAllPlugin.FeaturesAllFilter
 
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter
 
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByRangePlugin.FeaturesByRangeFilter
 
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByTagPlugin.FeaturesByTagFilter
 
FEATURES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
FEATURES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
FeatureSet - Class in com.github.seqware.queryengine.model
A feature set is a set (ex: collection, bag) of features.
FeatureSet() - Constructor for class com.github.seqware.queryengine.model.FeatureSet
Creates an instance of an anonymous feature set.
FeatureSet.Builder - Class in com.github.seqware.queryengine.model
 
FeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.FeatureSet.Builder
 
FEATURESET_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
featureSetID - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
FEATURESETIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
FeatureSetIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
FeatureSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
 
featureSets() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
 
featureSets() - Method in interface com.github.seqware.queryengine.model.Reference
Get the list of feature sets associated with this reference.
FeatureStoreInterface - Interface in net.sourceforge.seqware.queryengine.backend.store
 
FeatureTB - Class in com.github.seqware.queryengine.impl.tuplebinderIO
 
FeatureTB() - Constructor for class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
 
FeatureTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
FeatureTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
 
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
fields - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
 
fields - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
File - Class in net.sourceforge.seqware.common.model
 
File() - Constructor for class net.sourceforge.seqware.common.model.File
 
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES
 
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES
 
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES
 
FILE_EXPERIMENT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_EXPERIMENT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_EXPERIMENT_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_EXPERIMENT_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_FILE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_FILE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_IUS - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_IUS - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_IUS_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_IUS_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_IUS_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_IUS_TAG - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_IUS_TAG - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_LANE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_LANE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_LANE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_LANE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_LANE_NUMBER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_LANE_NUMBER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_LANE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_LANE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_LIBRARY - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_LIBRARY - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_META_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_META_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_PARENT_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_PARENT_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_PATH - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_PATH - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
 
FILE_PROCESSING_ALG - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_PROCESSING_ALG - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_PROCESSING_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_PROCESSING_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_RUN_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_RUN_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_RUN_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_RUN_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_SEQUENCER_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_SEQUENCER_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_SEQUENCER_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_SEQUENCER_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_STUDY_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_STUDY_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_STUDY_TITLE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_STUDY_TITLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
FILE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_TEMPLATE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_TEMPLATE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_TISSUE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_TISSUE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_WF_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_WF_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_WF_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_WF_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FILE_WF_VERSION - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
FILE_WF_VERSION - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
FileAttribute - Class in net.sourceforge.seqware.common.model
 
FileAttribute() - Constructor for class net.sourceforge.seqware.common.model.FileAttribute
 
FileAttribute(Integer) - Constructor for class net.sourceforge.seqware.common.model.FileAttribute
 
FileAttributeDAO - Interface in net.sourceforge.seqware.common.dao
 
FileAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
FileAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
 
FileAttributeResource - Interface in net.sourceforge.seqware.webservice.resources.tables
 
FileAttributeServerResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
FileAttributeServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
 
FileAttributeService - Interface in net.sourceforge.seqware.common.business
 
FileAttributeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
FileAttributeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
 
FileAttributesResource - Interface in net.sourceforge.seqware.webservice.resources.tables
 
FileAttributesServerResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
FileAttributesServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource
 
FileController - Class in net.sourceforge.solexatools.webapp.controller
LaneController
FileController() - Constructor for class net.sourceforge.solexatools.webapp.controller.FileController
 
FileController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.FileController
 
FileDAO - Interface in net.sourceforge.seqware.common.dao
 
FileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
FileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
FileDto - Class in net.sourceforge.seqware.webservice.dto
 
FileDto() - Constructor for class net.sourceforge.seqware.webservice.dto.FileDto
 
FILEEMPTY - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
fileExistsAndExecutable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
fileExistsAndNotEmpty(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
fileExistsAndReadable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
FileFinder - Class in net.sourceforge.solexatools.util
 
FileFinder() - Constructor for class net.sourceforge.solexatools.util.FileFinder
 
FileFinder(Pattern) - Constructor for class net.sourceforge.solexatools.util.FileFinder
 
FileIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
FileIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
 
FileLinker - Class in net.sourceforge.seqware.pipeline.plugins
 
FileLinker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
fileLinkReport() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
 
fileLinkReport(List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
 
fileLinkReport() - Method in interface net.sourceforge.seqware.common.business.ValidationReportService
Runs the ValidationReportService.fileLinkReport(List) including all files in the SeqWare meta db.
fileLinkReport(List<Integer>) - Method in interface net.sourceforge.seqware.common.business.ValidationReportService
Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study.
FileLinkReportResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
FileLinkReportResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource
 
FileList - Class in net.sourceforge.seqware.common.model.lists
 
FileList() - Constructor for class net.sourceforge.seqware.common.model.lists.FileList
 
FileMetadata - Class in net.sourceforge.seqware.common.module
This is a simple data structure to represent a file and it's metadata.
FileMetadata() - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
 
FileMetadata(String, String) - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
 
FileMetadata(String, String, String, String) - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
 
fileName - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
 
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
 
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
 
FILENOTEXECUTABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
FILENOTREADABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
FILENOTWRITABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
FileReportDAO - Interface in net.sourceforge.seqware.common.dao
 
FileReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
FileReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
FileReportRow - Class in net.sourceforge.seqware.common.model
 
FileReportRow() - Constructor for class net.sourceforge.seqware.common.model.FileReportRow
 
FileReportService - Interface in net.sourceforge.seqware.common.business
 
FileReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
FileReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
FileResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
FileResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.FileResource
 
FileResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
FileResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileResource
 
fileReverseHierarchyDisplay(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
 
fileReverseHierarchyDisplay(Integer) - Method in interface net.sourceforge.seqware.common.business.ValidationReportService
Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided fileSwa).
FileReverseHierarchyDisplayResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
FileReverseHierarchyDisplayResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource
 
files - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
files - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
files - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
filesArray - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
filesArray - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
FileService - Interface in net.sourceforge.seqware.common.business
 
FileServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
FileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
FileSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
FileSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.FileSetupController
 
filesFromExperiment(Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
FIXME: notice processings directly attached to study aren't examined!
filesFromIUS(IUS, Experiment, Sample, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
filesFromLane(Lane, Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
filesFromSample(Sample, Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
filesFromStudy(Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
FIXME: notice processings directly attached to study aren't examined!
filesFromStudy(Study) - Method in class net.sourceforge.seqware.common.hibernate.PropagateOwnership
 
FileTools - Class in net.sourceforge.seqware.common.util.filetools
 
FileTools() - Constructor for class net.sourceforge.seqware.common.util.filetools.FileTools
 
FileType - Class in net.sourceforge.seqware.common.model
 
FileType() - Constructor for class net.sourceforge.seqware.common.model.FileType
 
filetype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
 
filetype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
 
FILETYPE_ALL - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
FileTypeDAO - Interface in net.sourceforge.seqware.common.dao
 
FileTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
FileTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate
 
FileTypeService - Interface in net.sourceforge.seqware.common.business
 
FileTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
FileTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
 
FileUploadService - Interface in net.sourceforge.seqware.common.business
 
FileUploadServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
FileUploadServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
FileValidator - Class in net.sourceforge.solexatools.validation
 
FileValidator() - Constructor for class net.sourceforge.solexatools.validation.FileValidator
 
fillWorkflowProcessingMap(Processing, Map<WorkflowRun, Set<Processing>>) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
 
fillWorkflowProcessingMap(Processing, Map<WorkflowRun, Set<Processing>>) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
filter() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
 
filter() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
filter() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
FilteredExperimentResource - Class in net.sourceforge.seqware.webservice.resources.filters
 
FilteredExperimentResource() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.FilteredExperimentResource
 
filterFiles() - Method in class net.sourceforge.seqware.pipeline.decider.Decider
 
filterInit() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
 
filterInit() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
filterInit() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
filterReturnValues(List<ReturnValue>, String, String, boolean, boolean, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
filterReturnValuesV2(Writer, List<ReturnValue>, String, String, boolean, boolean, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
finalize() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
 
find(String, Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
find(String, Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
find(String, Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
find(String, Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
findAll(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
 
findAll(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
 
findAll(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
 
findAll(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
 
findAll(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
 
findAll(IUS) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO
 
findAll(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
 
findAll(Lane) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
 
findAll(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
 
findAll(Lane) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
 
findAll(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
 
findAll(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
 
findAll(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
 
findAll(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
 
findAll(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
 
findAll(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
 
findAll(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
 
findAll(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
 
findAll(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
 
findAll(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
 
findAll(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
 
findAll(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
 
findAll(String) - Method in class net.sourceforge.solexatools.util.FileFinder
 
findAll(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder
 
FindAllTheFiles - Class in net.sourceforge.seqware.common.hibernate
Should only be used for one query and then discarded and re-instantiated.
FindAllTheFiles() - Constructor for class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
FindAllTheFiles.Header - Enum in net.sourceforge.seqware.common.hibernate
 
findBelongsToStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
findBelongsToStudy(Study) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
findBelongsToStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
findBelongsToStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.FileService
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findByCriteria(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findByCriteria(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
findByCriteria(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
findByCriteria(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
findByEmailAddress(String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
Finds an instance of Registration in the database by the Registration emailAddress, and copies the Registration properties to an instance of RegistrationDTO.
findByEmailAddress(String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
 
findByEmailAddress(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
Finds an instance of Registration in the database by the Registration emailAddress only.
findByEmailAddress(String) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
 
findByEmailAddressAndPassword(String, String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
Finds an instance of Registration in the database by the Registration emailAddress and password, and copies the Registration properties to an instance of RegistrationDTO.
findByEmailAddressAndPassword(String, String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
 
findByEmailAddressAndPassword(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
Finds an instance of Registration in the database by the Registration emailAddress and password.
findByEmailAddressAndPassword(String, String) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
 
findByFilePath(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
Finds an instance of Processing in the database by the Processing emailAddress.
findByFilePath(String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.FileTypeService
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
 
findById(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.OrganismService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.PlatformService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
findById(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleSearchService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
Finds an instance of Experiment in the database by the Experiment ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
Finds an instance of ExperimentLibraryDesign in the database by the ExperimentLibraryDesign ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
Finds an instance of ExperimentSpotDesign in the database by the ExperimentSpotDesign ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
Finds an instance of ExperimentSpotDesignReadSpec in the database by the ExperimentSpotDesignReadSpec ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
Finds an instance of File in the database by the File ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
Finds an instance of SequencerRun in the database by the SequencerRun ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
Finds an instance of Project in the database by the Project ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
Finds an instance of Sample in the database by the Sample ID.
findById(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
Finds an instance of SequencerRun in the database by the SequencerRun ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
Finds an instance of ShareStudy in the database by the ShareStudy ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
Finds an instance of ShareWorkflowRun in the database by the ShareWorkflowRun ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
Finds an instance of Study in the database by the Study ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
Finds an instance of StudyType in the database by the StudyType ID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
findById(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
 
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
findByIDOnlyWithRunningWR(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
findByIDOnlyWithRunningWR(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
findByIDWithIUS(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findByIDWithIUS(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findByIDWithIUSAndRunningWR(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findByIDWithIUSAndRunningWR(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findByIDWithParams(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
findByIDWithParams(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Finds an instance of Lane in the database by the Lane emailAddress, and copies the Lane properties to an instance of Lane.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
Finds an instance of Project in the database by the Project emailAddress, and copies the Project properties to an instance of Project.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Finds an instance of Sample in the database by the Sample emailAddress, and copies the Sample properties to an instance of Sample.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Finds an instance of SequencerRun in the database by the SequencerRun emailAddress, and copies the SequencerRun properties to an instance of SequencerRun.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
Finds an instance of StudyType in the database by the StudyType emailAddress, and copies the StudyType properties to an instance of StudyType.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
findByName(String) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
findByName(String) - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
findByName(String) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
findByName(String) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
findByName(String) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
 
findByName(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findByName(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
Finds an instance of Lane in the database by the Lane emailAddress.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
Finds an instance of Project in the database by the Project name.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
Finds an instance of Sample in the database by the Sample emailAddress.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
Finds an instance of SequencerRun in the database by the SequencerRun name.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
Finds an instance of StudyType in the database by the StudyType name.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
 
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
 
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
findByOwnerId(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
findByOwnerId(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
findByOwnerId(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
findByOwnerId(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
findByPath(String) - Method in interface net.sourceforge.seqware.common.business.FileService
 
findByPath(String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
findByPath(String) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
findByPath(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
Finds an instance of File in the database by the File Path.
findByProcessingExperiment(Processing, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
findByProcessingExperiment(Processing, Experiment) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
 
findByProcessingExperiment(Processing, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
 
findByProcessingExperiment(Processing, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
 
findByProcessingIUS(Processing, IUS) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
findByProcessingIUS(Processing, IUS) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
 
findByProcessingIUS(Processing, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
 
findByProcessingIUS(Processing, IUS) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
 
findByProcessingLane(Processing, Lane) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
findByProcessingLane(Processing, Lane) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
 
findByProcessingLane(Processing, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
 
findByProcessingLane(Processing, Lane) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
 
findByProcessings(Processing, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
findByProcessings(Processing, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
 
findByProcessings(Processing, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
findByProcessings(Processing, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
 
findByProcessingSample(Processing, Sample) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
findByProcessingSample(Processing, Sample) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
 
findByProcessingSample(Processing, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
 
findByProcessingSample(Processing, Sample) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
 
findByProcessingSequencerRun(Processing, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
findByProcessingSequencerRun(Processing, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
 
findByProcessingSequencerRun(Processing, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
 
findByProcessingSequencerRun(Processing, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
 
findByProcessingStudy(Processing, Study) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
findByProcessingStudy(Processing, Study) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
 
findByProcessingStudy(Processing, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
 
findByProcessingStudy(Processing, Study) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
 
findByStudyIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
 
findByStudyIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
findByStudyIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
Finds an instance of ShareStudy in the database by the ShareStudy ID.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
findBySWAccession(Long) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
findBySWAccession(Long) - Method in interface net.sourceforge.seqware.common.business.LibraryService
Returns library matching given SeqWare Accession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
findBySWAccession(Long) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
findBySWAccession(Long) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
Returns library matching given SeqWare Accesssion.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
Finds an instance of Experiment in the database by the Experiment emailAddress, and copies the Experiment properties to an instance of Experiment.
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Finds an instance of Study in the database by the Study emailAddress, and copies the Study properties to an instance of Study.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
Finds an instance of Experiment in the database by the Experiment name.
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
Finds an instance of Sample in the database by the Experiment name.
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
Finds an instance of Study in the database by the Study name.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
 
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
Finds an instance of ShareWorkflowRun in the database by the ShareWorkflowRun ID.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
FindChildUtil - Class in net.sourceforge.solexatools.util
 
FindChildUtil() - Constructor for class net.sourceforge.solexatools.util.FindChildUtil
 
findDirectories(String) - Method in class net.sourceforge.solexatools.util.FileFinder
 
findDirectories(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder
 
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
findFiles(String) - Method in class net.sourceforge.solexatools.util.FileFinder
 
findFiles(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder
 
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
findFilesAssociatedWithASample(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
findFilesAssociatedWithASequencerRun(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
findFilesAssociatedWithAStudy(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
findFirstWorkflowClass(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder
 
findFor(Sample, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
Returns the Set of the Processings belongs to the specific Sample, WorkflowRun.
findFor(Sample) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
findFor(Sample, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
findFor(Sample) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
findIus() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusSearchResource
Locate IUS by sequencer run name, lane number and optionally sample name.
findIus() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource
 
FindRootUtil - Class in net.sourceforge.solexatools.util
 
FindRootUtil() - Constructor for class net.sourceforge.solexatools.util.FindRootUtil
 
findRunsForIUS(IUS) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findRunsForIUS(IUS) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
findRunsForIUS(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
findRunsForIUS(IUS) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
findRunsForSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
findRunsForSample(Sample) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
Find all the workflow runs for the specific sample.
findValueByID(WorkflowParam, Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
FINISHED - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun
 
finishTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
finishTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
FIRSTNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
fix_file_paths(String, ArrayList<String>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
Flat2TableTranscriptDB - Class in net.sourceforge.seqware.pipeline.modules.alignment
Given a set reference transcripts in flat files (fasta sequence file & a mapping/assocation file), create & populate database tables in UCSC format.
Flat2TableTranscriptDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
 
Flexigrid - Class in net.sourceforge.solexatools.webapp.metamodel
 
Flexigrid(int, int) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
Flexigrid(int) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
Flexigrid() - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
Flexigrid.Cells - Class in net.sourceforge.solexatools.webapp.metamodel
 
Flexigrid.Cells(List<String>) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
 
Flexigrid.ColumnModel - Class in net.sourceforge.solexatools.webapp.metamodel
 
Flexigrid.ColumnModel(String, String, int, boolean, String) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
flowcount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
 
flowcount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
 
flowsequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
 
flowsequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
 
flush() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Save all managed models to the back-end
flush(boolean) - Method in class com.github.seqware.queryengine.impl.HBaseModelManager
Normally, when doing a flush, we want to maintain the state of objects that
flush() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
flush(boolean) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Normally, when doing a flush, we want to maintain the state of objects that
flushObjects(List<Map.Entry<String, SimpleModelManager.AtomStatePair>>) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Flush objects to the back-end giving a working list
FOREVER - Static variable in interface com.github.seqware.queryengine.model.interfaces.TTLable
A time to set that means that the associated object should never expire
forJSON(String) - Static method in class net.sourceforge.seqware.common.util.jsontools.JsonUtil
 
forJSON(String) - Static method in class net.sourceforge.solexatools.util.ModelUtil
 
formatCode - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
frame - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
Freemarker - Class in net.sourceforge.seqware.common.util.freemarker
 
Freemarker() - Constructor for class net.sourceforge.seqware.common.util.freemarker.Freemarker
 
FREEMARKEREXCEPTION - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
FRIENDLY_ROWKEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
friendlyRowKey - Variable in class com.github.seqware.queryengine.util.SGID
this can be used to override the randomly generated IDs for the back-end.
fromBaseN(String, int) - Static method in class com.github.seqware.queryengine.kernel.Compression
Returns the integer extracted from the given string in a certain base.
fromDto(AttributeDto, Class<T>) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
fromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowReport
 
FSGID - Class in com.github.seqware.queryengine.util
Special class for Features which also stores the row key for features.
FSGID(long, long, long, String, String, SGID, boolean) - Constructor for class com.github.seqware.queryengine.util.FSGID
Create a fully functional FSGID given raw data
FSGID(SGID, FSGID) - Constructor for class com.github.seqware.queryengine.util.FSGID
construct a FSGID based on all the components of a SGID while taking the non-unique aspects on a FSGID, used when creating FeatureLists only
FSGID(SGID, Feature, FeatureSet) - Constructor for class com.github.seqware.queryengine.util.FSGID
Create a fully functional FSGID given models from the front-end
FSGIDIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
FSGIDIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO
 
fuzzyStartPositionMax - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
fuzzyStopPositionMin - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 

G

geneChr - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
GeneCountsRPKM - Class in net.sourceforge.seqware.pipeline.modules.quantification
Calculate read counts, coverage, & RPKM per transcript and gene given a BAM file of aligned reads.
GeneCountsRPKM() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
 
geneCoverage - Class in net.sourceforge.seqware.pipeline.modules.qc
To get coverage across transcript plot Underlying script: sw_module_CoverageAcrossTranscript.pl (by Sara Grimm) Necessary programs: perl, path to samtools Input: alignment file (bam) a map file, which is generated by the PrepTranscriptDB module, currently, ~/svnroot/seqware-complete/trunk/seqware-pipeline/data/annotation_reference/hg19_transcripts.hg19.20091027.trmap Expected output: coverage across transcript plot
geneCoverage() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
 
geneId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
geneId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
generateDax(Workflow, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.DaxgeneratorV2
 
generateDaxFile(WorkflowInfo, File, String, Map<String, String>, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
generateDaxFile(WorkflowInfo, File, String, Map<String, String>, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.PegasusWorkflowEngine
 
generateDefaultProfileElements() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
generateWorkflow(Workflow) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowInterface
 
GeneReportResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
GeneReportResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.GeneReportResource
 
GenericCommandRunner - Class in net.sourceforge.seqware.pipeline.modules
This is a very simple module that takes a few options on the command line and then passes the rest of the arguments to whatever command is specified.
GenericCommandRunner() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
 
GenericDBResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
GenericDBResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
 
GenericMetadataSaver - Class in net.sourceforge.seqware.pipeline.modules
This is a very simple module is used to save both a processing event and 0 or more files to the metadb.
GenericMetadataSaver() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
 
GenericQCGenome - Class in net.sourceforge.seqware.pipeline.modules.qc
Estimate % of reads in a given lane that align to a specified set of sequence databases.
GenericQCGenome() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
 
GenericTemplateResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
GenericTemplateResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
genomeId - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
genomeTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
genomicSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
get() - Method in class com.github.seqware.queryengine.model.Analysis
 
get() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
 
get(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
get() - Method in interface com.github.seqware.queryengine.model.QueryFuture
Blocking call to retrieve results of a query
get(String) - Method in interface com.github.seqware.queryengine.model.TagSet
 
get() - Method in class com.github.seqware.queryengine.util.LazyLatestReference
Retrieve the lazy referenced object if possible and return it
get() - Method in class com.github.seqware.queryengine.util.LazyReference
Retrieve the lazy referenced object if possible and return it
get(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
 
get(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
 
get(File) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
 
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
 
get(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
 
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
 
get(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
 
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
 
get(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
 
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
 
get(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
 
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
 
get(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
 
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
 
get() - Static method in class net.sourceforge.seqware.common.factory.DBAccess
 
get(String, String, boolean) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
 
get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
 
get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
 
get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
 
get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
 
get() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
 
get_description() - Method in class net.sourceforge.seqware.pipeline.decider.Decider
 
get_description() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
get_description() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
 
get_galaxy_xml() - Method in class net.sourceforge.seqware.pipeline.module.Module
Output Galaxy definition files so you can use this module with Galaxy.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.decider.Decider
 
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Generates a "help" message for the user of the plugin.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.module.Module
A method used to return the syntax for this module
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.Picard
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
A method used to return the syntax for this module
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Generates a "help" message for the user of the plugin.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
get_workflow_info(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
get_workflow_run_accession(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
get_workflow_run_id(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getABISOLID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Gets the value of the abisolid property.
getAbstractStr() - Method in class net.sourceforge.seqware.common.model.Study
 
getABUNDANCEMEASUREMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the abundancemeasurement property.
getAccess() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get whether 0) owner can read, 1) owner can write, 2) group can read, 3) group can write, 4) other users can read 5) other users can write
getAccession() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getAccession() - Method in class net.sourceforge.seqware.common.model.Organism
 
getAccession() - Method in class net.sourceforge.seqware.common.model.Study
 
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the accession property.
getAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getAcl() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
getAclBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getAclOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getAclOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getAclOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
getACLs() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getACTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS
Gets the value of the action property.
getACTIONS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the actions property.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
getActive() - Method in class net.sourceforge.seqware.common.model.ShareFile
 
getActive() - Method in class net.sourceforge.seqware.common.model.ShareLane
 
getActive() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
getActive() - Method in class net.sourceforge.seqware.common.model.ShareSample
 
getActive() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
getActive() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
getAdapters() - Method in class net.sourceforge.seqware.common.model.Sample
 
getAdapterSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
getADAPTERSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Gets the value of the adapterspec property.
getADD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the add property.
getAddedSurcharge() - Method in class net.sourceforge.seqware.common.model.Expense
 
getAdditionalAttribute(String) - Method in class com.github.seqware.queryengine.model.Feature
Returns the value of an additional attribute or null of the attribute does not exist.
getAdditionalAttributeNames() - Method in class com.github.seqware.queryengine.model.Feature
Returns the names of the additional attributes stored.
getAdhoctagset() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getAgent() - Method in class net.sourceforge.seqware.common.model.Expense
 
getAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing
 
getAlgorithm() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
getAlgorithm() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
 
getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
 
getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
getAlias() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getAlias() - Method in class net.sourceforge.seqware.common.model.IUS
 
getAlias() - Method in class net.sourceforge.seqware.common.model.Sample
 
getAlias() - Method in class net.sourceforge.seqware.common.model.Study
 
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the alias property.
getAlign() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
getAligners() - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
getAligners(int) - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
getAligners() - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
getAligners(int) - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
getAligners() - Static method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
getAligners(int) - Static method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
getAll() - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
 
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
 
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
 
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
 
getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
 
getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
 
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.StorageInterface
For debugging or very non-optimal implementations
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
getAllAtomsForTable(String) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.StorageInterface
Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
getAllHtml(Lane, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
getAllHtml(IUS, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
 
getAllHtml(IUS, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
 
getAllHtml(Study, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getAllHtml(Experiment, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getAllHtml(Sample, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getAllHtml(Lane, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getAllItems() - Method in class net.sourceforge.solexatools.util.PageInfo
 
getAllProcessing() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getAllProcessings() - Method in class net.sourceforge.seqware.common.model.Lane
 
getAllRuns() - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.
getAllSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
Get all selected Files, the files are organized by the name of the parameter (key) and a list of files selected (value) via a hash.
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getAllStudies() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getANALYSIS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet
Gets the value of the analysis property.
getANALYSISATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES
Gets the value of the analysisattribute property.
getANALYSISATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysisattributes property.
getAnalysisCenter() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysisCenter property.
getANALYSISFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysisfiles property.
getAnalysisIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAnalysisIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getAnalysisIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getAnalysisIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAnalysisIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAnalysisIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAnalysisIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getAnalysisIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getAnalysisIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAnalysisIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getAnalysisIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getAnalysisIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAnalysisIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getAnalysisIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getAnalysisIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAnalysisIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getAnalysisIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getANALYSISLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS
Gets the value of the analysislink property.
getANALYSISLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysislinks property.
getAnalysisPlugins() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getAnalysisPlugins() - Method in interface com.github.seqware.queryengine.model.QueryInterface
 
getAnalysisPlugins() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getAnalysisSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
getAnalysisSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getAnalysisSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface
 
getAnalysisSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getANALYSISTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysistype property.
getAnalysisWorkflowHtml(WorkflowRun, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getAnonymizedName() - Method in class net.sourceforge.seqware.common.model.Sample
 
getANONYMIZEDNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Gets the value of the anonymizedname property.
getApplication() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
 
getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
 
getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
 
getArch() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
getArgs(String) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
 
getArgs(String, boolean) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
 
getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
 
getAsText() - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getAtomBySGID(SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getAtomBySGID(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getAtomBySGID(SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Deprecated. It is much more efficient to retrieve an Atom when you know the class
getAtomBySGID(Class<T>, SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Find an object in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getAtomsBySGID(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getAtomsBySGID(Class<T>, SGID...) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Find a batch of objects in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAttribute(String) - Method in class com.github.seqware.queryengine.model.Feature
Generic implementation for retrieving the value of a GVF or additional attribute.
getAttribute(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
 
getAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
 
getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
 
getAttributes() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
 
getBackEnd() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Get a reference to the currently operating back-end
getBackendTimestamp() - Method in class com.github.seqware.queryengine.util.SGID
 
getBarcode() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getBarcodeSeqence() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Gets the value of the barcodeSeqence property.
getBaseCaller() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getBASECALLER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
Gets the value of the basecaller property.
getBASECALLS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
Gets the value of the basecalls property.
getBaseCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getBASECOORD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the basecoord property.
getBaseDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getBaseIniFile() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getBaseQualities() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getBatch_size() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getBinSize() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getBinSize() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getBlockCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getBlockSizes() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getBlockStarts() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getBrokerName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the brokerName property.
getBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getBundleInfo(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
getCacheSize() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getCalledBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getCalledBaseCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getCalledBaseCountForward() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getCalledBaseCountReverse() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getCallOne() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getCallTwo() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getCascade() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
getCascade() - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet
 
getCascade() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
getCascade() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return whether cascade should occur on deletion
getCell() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
 
getCenterName() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getCenterName() - Method in class net.sourceforge.seqware.common.model.Study
 
getCenterName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the centerName property.
getCENTERNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the centername property.
getCenterName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the centerName property.
getCenterProjectName() - Method in class net.sourceforge.seqware.common.model.Study
 
getCENTERPROJECTNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the centerprojectname property.
getChecksum() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Gets the value of the checksum property.
getChecksumMethod() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Gets the value of the checksumMethod property.
getChildMaps() - Method in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
getChildren() - Method in class net.sourceforge.seqware.common.model.Processing
 
getChildren() - Method in class net.sourceforge.seqware.common.model.Sample
 
getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
getChildrenUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getChildSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getChildSample() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
getChildSample() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getChildSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getChildSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getChildTags() - Method in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
getClassesDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getClientNotes() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getCode() - Method in class net.sourceforge.seqware.common.model.Organism
 
getCode() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
 
getCodingStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getCodingStop() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getCOLOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
Gets the value of the color property.
getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getCOLORMATRIX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Gets the value of the colormatrix property.
getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getCOLORMATRIXCODE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Gets the value of the colormatrixcode property.
getCommand() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getCommand() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getCommand() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getCommandOutput() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
getCOMMONNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Gets the value of the commonname property.
getCompleted() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getComputeReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getConfigPath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
 
getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
 
getConfirmEmailAddress() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
 
getConfirmPassword() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
 
getConnectionString() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getConsensusAveSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getConsensusBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getConsensusCallQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getConsensusMaxSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
The consequenceID should be of the form: "..consequence....v" for example "hg18.chr12:00230.consequence.genome1212.G.ak21219.v1"
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getConsequence(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
Since both variants and consequences are stored under the same ID based on location this really doesn't make a lot of sense.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getConsequencesByMismatch(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getConsequencesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getConstructionProtocol() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getCONTACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS
Gets the value of the contact property.
getCONTACTS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the contacts property.
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
 
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getContig() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
getCount() - Method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet
 
getCount() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
getCount() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
getCount() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
getCount() - Method in class com.github.seqware.queryengine.util.InMemoryIterable
 
getCount() - Method in interface com.github.seqware.queryengine.util.SeqWareIterable
Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.util.SGIDIterable
 
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
 
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Not supported for HBase backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Not supported for HBase backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
 
getCount() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator
 
getCountFile() - Method in class net.sourceforge.seqware.common.model.Sample
 
getCountFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
getCountFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
getCountFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
getCountFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
getCoverage(Integer) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
getCoverage() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
Calling function will get back the coverage blocks that are contained within the range of interest so make sure it pads +/- the bin size in the requested range otherwise may miss data!
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
Calling function will get back the coverage blocks that are contained within the range of interest so make sure it pads +/- the bin size in the requested range otherwise may miss data!
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
Calling function will get back the coverage blocks that are contained within the range of interest so make sure it pads +/- the bin size in the requested range otherwise may miss data!
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getCoverages(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getCoverages(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getCreated() - Method in class net.sourceforge.seqware.common.model.SampleSearch
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Project
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile
 
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane
 
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample
 
getCriteria() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
 
getCurrentSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
getCurrentSelectedNodes(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
getCurrentWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
getCurrentWorkflowParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
getCurrentWorkingDir() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
 
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Not applicable for HBase backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Not applicable for HBase backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
 
getCursor() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator
 
getCwd() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getCycleCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getCYCLECOORD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the cyclecoord property.
getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getCYCLECOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Gets the value of the cyclecount property.
getCYCLECOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Gets the value of the cyclecount property.
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.Lane
 
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getCYCLESEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Gets the value of the cyclesequence property.
getData() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
getDatabase() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getDATABLOCK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the datablock property.
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getDate() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getDax() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getDaysUntilDue() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getDb() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getDb() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
getDb() - Method in class net.sourceforge.seqware.common.model.IUSLink
 
getDb() - Method in class net.sourceforge.seqware.common.model.LaneLink
 
getDb() - Method in class net.sourceforge.seqware.common.model.SampleLink
 
getDb() - Method in class net.sourceforge.seqware.common.model.StudyLink
 
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
Gets the value of the db property.
getDbmd() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getDecodeMethod() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
getDecryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Gets cipher by DecryptKey.
getDecryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
getDefaultDirManagerExcutable(Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowExecutableUtils
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getDefaultJavaArguments(Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.ArgumentUtils
 
getDefaultJavaExcutable(Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowExecutableUtils
 
getDefaultPerlExcutable(Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowExecutableUtils
 
getDefaultSeqwareExecutable(Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowExecutableUtils
 
getDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getDENOVOASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the denovoassembly property.
getDependentElement(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getDescription() - Method in interface com.github.seqware.queryengine.model.AnalysisSet
Get the description associated with this analysisSet
getDescription() - Method in class com.github.seqware.queryengine.model.FeatureSet
Get the description associated with this FeatureSet
getDescription() - Method in interface com.github.seqware.queryengine.model.Group
Get the description associated with this group
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet
 
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
getDescription() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Expense
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getDescription() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getDescription() - Method in class net.sourceforge.seqware.common.model.File
 
getDescription() - Method in class net.sourceforge.seqware.common.model.IUS
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Lane
 
getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
getDescription() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Platform
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Processing
 
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Project
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Sample
 
getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Study
 
getDescription() - Method in class net.sourceforge.seqware.common.model.StudyType
 
getDescription() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getDescription() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getDescription() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getDescription() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the description property.
getDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the description property.
getDescription() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
getDescription() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getDescriptor() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the descriptor property.
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getDescriptorForType() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getDESIGN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the design property.
getDESIGNDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Gets the value of the designdescription property.
getDibase() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
Gets the value of the dibase property.
getDirContext() - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
 
getDirectoriesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder
 
getDirectorySize() - Method in class net.sourceforge.solexatools.util.FileFinder
 
getDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getDisplay() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
getDisplayName() - Method in class net.sourceforge.seqware.common.model.FileType
 
getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
getDisplayName() - Method in class net.sourceforge.solexatools.util.SummaryLine
 
getDisplayValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getDomainObject() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
 
getDomainObject() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
 
getEmail() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
 
getEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getEmailAddress() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getEmailAddress() - Method in class com.github.seqware.queryengine.model.User
Get email address
getEmailAddress() - Method in class net.sourceforge.seqware.common.model.Registration
 
getEncryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Gets cipher by EncryptKey.
getEncryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
getEnd() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getEndDate() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getEndPage() - Method in class net.sourceforge.solexatools.util.PageInfo
 
getEntityUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
Gets the value of the entrezlink property.
getError() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
 
getErrorCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
getErrorCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.Lane
 
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getErrorCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getExistingStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
Gets the value of the existingStudyType property.
getExistingType() - Method in class net.sourceforge.seqware.common.model.Study
 
getExistingTypeInt() - Method in class net.sourceforge.seqware.common.model.Study
 
getExitCode() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
 
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SeqwareException
 
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadFileException
 
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadModuleException
 
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwParameterException
 
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwRunnerParameterException
 
getExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing
 
getExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getExpectedBaseCall() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getEXPECTEDBASECALL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the expectedbasecall property.
getExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpectedNumberReads() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the expectedNumberReads property.
getExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpectedNumberRuns() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the expectedNumberRuns property.
getExpectedNumberSpots() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpectedNumberSpots() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the expectedNumberSpots property.
getExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample
 
getExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample
 
getExpectedNumSpots() - Method in class net.sourceforge.seqware.common.model.Sample
 
getExpenseId() - Method in class net.sourceforge.seqware.common.model.Expense
 
getExpenses() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getExpenseType() - Method in class net.sourceforge.seqware.common.model.Expense
 
getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
getExperiment() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getExperiment() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
getExperiment() - Method in class net.sourceforge.seqware.common.model.Sample
 
getExperiment() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
getEXPERIMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet
Gets the value of the experiment property.
getEXPERIMENTATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES
Gets the value of the experimentattribute property.
getExperimentAttributeId() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
getExperimentAttributes() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getEXPERIMENTATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the experimentattributes property.
getExperimentHtml(Experiment, Registration, String, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getExperimentId() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExperimentLibraryDesign() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExperimentLibraryDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getExperimentLibraryDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getEXPERIMENTLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS
Gets the value of the experimentlink property.
getExperimentLinkId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
getExperimentLinks() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getEXPERIMENTLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the experimentlinks property.
getEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the experimentref property.
getEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the experimentref property.
getExperiments() - Method in class net.sourceforge.seqware.common.model.Processing
 
getExperiments() - Method in class net.sourceforge.seqware.common.model.Study
 
getExperimentService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getExperimentService() - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getExperimentSpotDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
getExperimentSpotDesignReadSpecId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getExperimentSpotDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getExperimentSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getExpiryDate() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
getExpiryDate() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return the expiry date
getExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getExpiryTime() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
getExpiryTime() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
getExpiryTime() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return raw expiry time
getExpLibDesignDesc() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpLibDesignName() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpLibDesignProtocol() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpLibDesignSelection() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpLibDesignSource() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpLibDesignStrategy() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpSpotDesignAdapterSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpSpotDesignReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExpSpotDesignTagSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getExtension() - Method in class net.sourceforge.seqware.common.model.FileType
 
getExtension(String) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
getExternalId() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getExternalSerializationVersion() - Method in interface com.github.seqware.queryengine.model.Atom
Get the serializationVersion for this particular atom.
getExternalSerializationVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
getFailed() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getFailedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
getFailedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
getFailedJobsInfo(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
This method will examine a Pegasus DAX log directory for a given workflow and identify the log files for jobs that failed.
getFastqConvNum() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getFastqConvNum() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getFeature() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getFeature(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
The featureID should be of the form: "..feature..v" for example "hg18.chr12:00230.feature.genome1212.v1"
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getFeature(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeatures(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeatures(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeatures(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
 
getFeatures(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getFeatures() - Method in class com.github.seqware.queryengine.model.FeatureSet
Get the list of features associated with this feature set.
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
Returns a list of features at this location, should not be modified.
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
getFeatures(int, FeatureSet) - Method in interface com.github.seqware.queryengine.model.QueryInterface
(Do not) filter features
getFeatures(String, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This doesn't do bounds checking on the stop, the client will need to close the iterator when it reaches the requested end!
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getFeatures() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getFeatures(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
 
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Filter features by a range of attributes.
getFeaturesByPlugin(int, Class<? extends AnalysisPluginInterface>, FeatureSet, Object...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getFeaturesByPlugin(int, Class<? extends AnalysisPluginInterface>, FeatureSet, Object...) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Call an arbitrary installed plug-in by class and initiate it
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
 
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in interface com.github.seqware.queryengine.model.QueryInterface
filter features that overlap with a given range
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
 
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in interface com.github.seqware.queryengine.model.QueryInterface
filter features with tags.
getFeaturesByTag(String, Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer, String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getFeaturesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeaturesCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeaturesCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getFeatureSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getFeatureSetBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getFeatureSetCount(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
 
getFeatureSetCount(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getFeatureSetCount(int, FeatureSet) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Get the number of features in a feature set
getFeatureSetID() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getFeatureSetID() - Method in class com.github.seqware.queryengine.util.FSGID
Get the ID for the associated feature set
getFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getFeatureSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getFeatureSetOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getFeatureSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
getFeatureSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getFeatureSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface
 
getFeatureSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeaturesList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeaturesList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeaturesOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeaturesOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeaturesOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeaturesOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getFeaturesTags() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getFeaturesUnordered() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getFile() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getFile(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getFile() - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
getFile() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getFile() - Method in class net.sourceforge.seqware.common.model.ShareFile
 
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES
Gets the value of the file property.
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES
Gets the value of the file property.
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES
Gets the value of the file property.
getFile() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
getFileAttributeId() - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
getFileAttributes(Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
Returns a complete set of attributes for a give File.
getFileAttributes(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
 
getFileAttributes() - Method in class net.sourceforge.seqware.common.model.File
 
getFileAttributes() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributesResource
 
getFileAttributes() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource
 
getFileAttributeService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getFileAttributeService() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getFileHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
getFileHtml(Processing, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
 
getFileHtml(Processing, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
 
getFileId() - Method in class net.sourceforge.seqware.common.model.File
 
getFileMetaType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getFileMetaType() - Method in class net.sourceforge.solexatools.util.SummaryLine
 
getFilename() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getFileName() - Method in class net.sourceforge.seqware.common.model.File
 
getFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Gets the file name.
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
Gets the value of the filename property.
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
Gets the value of the filename property.
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Gets the value of the filename property.
getFileName(String) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
 
getFileOne() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getFilePath() - Method in class net.sourceforge.seqware.common.model.File
 
getFilePath() - Method in class net.sourceforge.seqware.common.model.Processing
 
getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getFilePath() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getFilePath() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getFilePath(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getFilePath() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.FileService
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
WITH RECURSIVE "processing_root_to_leaf" ("child_id", "parent_id") AS ( SELECT p."child_id" as "child_id", p."parent_id" FROM "processing_relationship" p where p."parent_id" = 53851 UNION ALL SELECT p."child_id", rl."parent_id" FROM "processing_root_to_leaf" rl, "processing_relationship" p WHERE p."parent_id" = rl."child_id" ) --select * from "processing_root_to_leaf" p; select distinct file_id from "processing_root_to_leaf"p, processing_files pf where p.parent_id = processing_id or p.child_id = processing_id;
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
getFiles() - Method in class net.sourceforge.seqware.common.model.Processing
 
getFiles() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getFiles() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the files property.
getFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the files property.
getFiles(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
getFiles() - Method in class net.sourceforge.solexatools.util.SummaryLine
 
getFiles_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getFilesArray() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
getFileService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getFileService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
getFileService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
getFileServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getFileSize(String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
getFilesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder
 
getFileSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getFileTwo() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getFileTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getFileType() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getFileType() - Method in class net.sourceforge.seqware.common.model.File
 
getFileType() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getFiletype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
Gets the value of the filetype property.
getFiletype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
Gets the value of the filetype property.
getFileTypeId() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getFileTypeId() - Method in class net.sourceforge.seqware.common.model.FileType
 
getFileTypeId() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
 
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
 
getFileUploadService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getFileURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getFileURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getFileValidationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesAllPlugin
 
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin
 
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
 
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByRangePlugin
 
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByTagPlugin
 
getFinalDestination() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getFinalResult() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
Blocking call to get the final result of the plug-in
getFinalResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
getFinalResult() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
 
getFinalResult() - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin
 
getFinishedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
getFinishedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
getFinishedTimestamp() - Method in class net.sourceforge.seqware.common.model.Expense
 
getFirstId(String) - Static method in class net.sourceforge.solexatools.util.Constant
 
getFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getFirstName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getFirstName() - Method in class com.github.seqware.queryengine.model.User
Get first name
getFirstName() - Method in class net.sourceforge.seqware.common.model.Registration
 
getFirstName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
 
getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getFLOWCOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Gets the value of the flowcount property.
getFLOWCOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Gets the value of the flowcount property.
getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getFLOWSEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Gets the value of the flowsequence property.
getFLOWSEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Gets the value of the flowsequence property.
getFolderStore() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getFolderStore() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getForceRunAll() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getFormatCode() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the formatCode property.
getFrame() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getFriendlyRowkey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
getFriendlyRowKey() - Method in class com.github.seqware.queryengine.util.SGID
 
getFullName() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getFuzzyStartPositionMax() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getFuzzyStopPositionMin() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getGeneChr() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getGeneId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getGeneId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getGenomeId() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getGenomicSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getGroup() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get the group for the object
getGroup() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getGroups() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
getGroups() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getGroups() - Method in interface com.github.seqware.queryengine.model.QueryInterface
Get all groups
getGroups() - Method in class com.github.seqware.queryengine.model.User
Get list of groups that this user is a part of
getGroups() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getGroupSGID() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get the group for the object
getGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getGrp() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getGrpBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getGrpOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getGrpOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getGrpOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrps(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getGrpsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrpsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getGrpsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrpsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getGrpsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrpsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getGrpsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrpsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getHandle() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the handle property.
getHBaseClass() - Method in class com.github.seqware.queryengine.model.Feature
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.Tag
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.User
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.Feature
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.Tag
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.User
 
getHeader() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getHeader() - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
 
getHELICOS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Gets the value of the helicos property.
getHOLD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the hold property.
getHoldForPeriod() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Gets the value of the holdForPeriod property.
getHoldUntilDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Gets the value of the holdUntilDate property.
getHost() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getHost() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getHost() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getHtml() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getHtml() - Method in class net.sourceforge.seqware.common.model.Study
 
getHtml() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
 
getHtml(Object, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getHtml(WorkflowRun, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
 
getHtml(Sample, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
 
getHtml(Processing, WorkflowRun, Registration, String, List<String>, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
 
getHttpInputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
getHYBRIDASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the hybridassembly property.
getId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getId() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getId() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
getId() - Method in class net.sourceforge.seqware.common.model.IUSLink
 
getId() - Method in class net.sourceforge.seqware.common.model.LaneLink
 
getId() - Method in class net.sourceforge.seqware.common.model.SampleLink
 
getId() - Method in class net.sourceforge.seqware.common.model.StudyLink
 
getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
 
getId() - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface
 
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.StringId
 
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
Gets the value of the id property.
getId() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
 
getId(String) - Static method in class net.sourceforge.solexatools.util.Constant
 
getIdentitySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
getIdsSelectedLane(HttpServletRequest, WorkflowParam) - Method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
getILLUMINA() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Gets the value of the illumina property.
getIndividualName() - Method in class net.sourceforge.seqware.common.model.Sample
 
getInfo() - Method in class net.sourceforge.seqware.common.model.FileType
 
getInfo() - Method in class net.sourceforge.solexatools.util.PageInfo
 
getInformOnError() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Gets the value of the informOnError property.
getInformOnStatus() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Gets the value of the informOnStatus property.
getIniFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getInput() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getInput() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getInputAlgorithm() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getInputFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getInputFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusSeqwareModuleJob
 
getInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
getInstance() - Static method in class net.sourceforge.seqware.common.ContextImpl
 
getInstance() - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowContext
 
getInstitution() - Method in class net.sourceforge.seqware.common.model.Registration
 
getInstitution() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
 
getInstrumentModel() - Method in class net.sourceforge.seqware.common.model.Platform
 
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Gets the value of the instrumentmodel property.
getInstrumentModel() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the instrumentModel property.
getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getInstrumentName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the instrumentName property.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
Internal parameters that can be used to pass information to the Mapper and Reducers.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesAllPlugin
 
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByAttributesPlugin
 
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByRangePlugin
 
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByTagsPlugin
 
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin
 
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin
 
getInvitationCode() - Method in class net.sourceforge.seqware.common.model.Registration
 
getInvoice() - Method in class net.sourceforge.seqware.common.model.Expense
 
getInvoiceId() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
 
getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
 
getIsEnd() - Method in class net.sourceforge.solexatools.util.PageInfo
 
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.IUS
 
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Lane
 
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Processing
 
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Sample
 
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Study
 
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getIsInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
 
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getIsSelected() - Method in class net.sourceforge.seqware.common.model.File
 
getIsSelected() - Method in class net.sourceforge.seqware.common.model.IUS
 
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Lane
 
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Processing
 
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Sample
 
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Study
 
getIsSelected() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getIsStart() - Method in class net.sourceforge.solexatools.util.PageInfo
 
getItemRgb() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getIus() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getIus() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
getIus() - Method in class net.sourceforge.seqware.common.model.IUSLink
 
getIus() - Method in class net.sourceforge.seqware.common.model.Lane
 
getIUS() - Method in class net.sourceforge.seqware.common.model.Lane
 
getIUS() - Method in class net.sourceforge.seqware.common.model.Processing
 
getIus() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
getIUS() - Method in class net.sourceforge.seqware.common.model.Sample
 
getIus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
getIus() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
getIus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
 
getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
getIusAttributeId() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
getIusAttributes() - Method in class net.sourceforge.seqware.common.model.IUS
 
getIusFiles() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusFilesResource
List files associated with Ius.
getIusFiles() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource
 
getIUSHtml(IUS, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getIusId() - Method in class net.sourceforge.seqware.common.model.IUS
 
getIusLinkId() - Method in class net.sourceforge.seqware.common.model.IUSLink
 
getIusLinks() - Method in class net.sourceforge.seqware.common.model.IUS
 
getIusService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getIusSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getIusSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getIusTag() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getJobArgument() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getJobById(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getJobModule() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
getJobs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getJobsByAlgo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
 
getJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
 
getJsonEscapeAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing
 
getJsonEscapeDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.File
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.IUS
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Lane
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Processing
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Sample
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Study
 
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Study
 
getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
getJsonEscapeFileName() - Method in class net.sourceforge.seqware.common.model.File
 
getJsonEscapeFullName() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getJsonEscapeKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.IUS
 
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Lane
 
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Sample
 
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Sample
 
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Study
 
getJsonEscapeType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
getKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getKey() - Method in class com.github.seqware.queryengine.model.Tag
Get the key.
getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
 
getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
 
getKeyIndex() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getKeyValueFromFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
getKeyvalues() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
 
getLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
getLabel() - Method in class net.sourceforge.seqware.common.model.IUSLink
 
getLabel() - Method in class net.sourceforge.seqware.common.model.LaneLink
 
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
getLabel() - Method in class net.sourceforge.seqware.common.model.SampleLink
 
getLabel() - Method in class net.sourceforge.seqware.common.model.StudyLink
 
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
Gets the value of the label property.
getLabName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the labName property.
getLane() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getLane() - Method in class net.sourceforge.seqware.common.model.IUS
 
getLane() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
getLane() - Method in class net.sourceforge.seqware.common.model.LaneLink
 
getLane() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
getLane() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
getLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
getLane() - Method in class net.sourceforge.seqware.common.model.ShareLane
 
getLane() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
 
getLane1() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLane2() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLane3() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLane4() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLane5() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLane6() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLane7() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLane8() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLane_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getLaneAttributeId() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
getLaneAttributes() - Method in class net.sourceforge.seqware.common.model.Lane
 
getLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
 
getLaneHtml(Lane, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getLaneHtml(Lane, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getLaneId() - Method in class net.sourceforge.seqware.common.model.Lane
 
getLaneIndex() - Method in class net.sourceforge.seqware.common.model.Lane
 
getLaneLinkId() - Method in class net.sourceforge.seqware.common.model.LaneLink
 
getLaneLinks() - Method in class net.sourceforge.seqware.common.model.Lane
 
getLaneName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getLanes() - Method in class net.sourceforge.seqware.common.model.Processing
 
getLanes() - Method in class net.sourceforge.seqware.common.model.Sample
 
getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getLanes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getLaneService() - Method in class net.sourceforge.solexatools.validation.LaneValidator
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
getLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getLaneSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getLaneSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getLastName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getLastName() - Method in class com.github.seqware.queryengine.model.User
Get last name
getLastName() - Method in class net.sourceforge.seqware.common.model.Registration
 
getLastName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
 
getLatestAtomByRowKey(String, Class<T>) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getLatestAtomByRowKey(String, Class<T>) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Find an atom in the back-end when a specific class is known and a specific row key is known
getLatestAtomBySGID(SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getLatestAtomBySGID(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getLatestAtomBySGID(SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Deprecated. It is much more efficient to retrieve an Atom when you know the class
getLatestAtomBySGID(SGID, Class<T>) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Find an object in the back-end when a specific class is known while ignoring the timestamp
getLatestModel(String, TupleBinding, HTable, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This is actually a pretty dangerous method since just the most recent biallelic variant will be returned.
getLayout() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getLeastSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
getLength() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getLibraries() - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
 
getLibraries(Map<String, String>) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
 
getLibraries() - Method in interface net.sourceforge.seqware.common.business.LibraryService
Returns a complete list of libraries.
getLibraries(Map<String, String>) - Method in interface net.sourceforge.seqware.common.business.LibraryService
Returns a list of libraries that match all attributes provided in the give attributes Map.
getLibraries(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
 
getLibraries() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
 
getLibraries(String, String) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
Returns list of libraries that contain the attribute attributeName=attributeValue.
getLibraries() - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
Returns a complete list of libraries.
getLibraries() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource
 
getLIBRARYCONSTRUCTIONPROTOCOL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the libraryconstructionprotocol property.
getLIBRARYDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Gets the value of the librarydescriptor property.
getLibraryId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
 
getLIBRARYLAYOUT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the librarylayout property.
getLIBRARYNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the libraryname property.
getLibrarySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
getLIBRARYSELECTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the libraryselection property.
getLibrarySelectionId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
getLibraryService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getLibraryServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getLIBRARYSOURCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the librarysource property.
getLibrarySourceId() - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
getLIBRARYSTRATEGY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the librarystrategy property.
getLibraryStrategyId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
getLibraryType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.FileList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.IUSList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.LaneList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.SampleList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
 
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
 
getLocalJavaExcutable(Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowExecutableUtils
 
getLocatableModels(SecondaryDatabase, TupleBinding, String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getLocatableModels(String, String, TupleBinding, String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getLock() - Method in class com.github.seqware.queryengine.system.importers.Importer
 
getLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. Lock file, do not clear on exit
getLock(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. Lock file, but give option to free lock when the JVM exits.
getLock(int, int) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated.  
getLock() - Method in class net.sourceforge.seqware.queryengine.tools.importers.Importer
 
getLongName() - Method in class net.sourceforge.seqware.common.model.Platform
 
getLS454() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Gets the value of the ls454 property.
getManager() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the model manager for this Atom
getMap() - Method in class com.github.seqware.queryengine.util.obo.OboFileHandlerHack
 
getMaxCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getMaxCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getMaxCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
getMaximumMappingQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getMaxLockers() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getMaxLockObjects() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getMaxLocks() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getMD5Hash(String) - Method in class net.sourceforge.seqware.common.metadata.Metadata
 
getMd5sum() - Method in class net.sourceforge.seqware.common.model.File
 
getMd5sum() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
getMeaning() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
 
getMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF
Gets the value of the member property.
getMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS
Gets the value of the member property.
getMEMBERS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the members property.
getMemReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getMetadata() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
getMetadata() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
getMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getMetaType() - Method in class net.sourceforge.seqware.common.model.File
 
getMetaType() - Method in class net.sourceforge.seqware.common.model.FileType
 
getMetaType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getMetaType() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getMetaType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
getMinCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getMinCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getMinCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
getMinObservations() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
getMinObservationsPerStrand() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
getMinPercent() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
getMinSnpQuality() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getMinSnpQuality() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getMinSNVPhred() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
The mismatchID should be of the form: "..variant...v" for example "hg18.chr12:00230.variant.genome1212.G.v1"
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getMismatch(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getMismatchAAChangeBlosumScore() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMismatchAminoAcidChange() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMismatchChr() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMismatchCodonChange() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMismatchCodonPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This doesn't do bounds checking on the stop, the client will need to close the iterator when it reaches the requested end!
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getMismatches() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getMismatches(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getMismatches(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getMismatches() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
 
getMismatches() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
 
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getMismatchesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getMismatchesTags() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getMismatchesUnordered() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getMismatchId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMismatchStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMismatchStop() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
Get access to an iterator containing all the mismatch tags.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
Get access to an iterator containing all the mismatch tags.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getMismatchType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getModel(String, TupleBinding, HTable, String, String, Long) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getModel(String, String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getModelAndView(String, ModelAndView) - Static method in class net.sourceforge.solexatools.util.StudyBuildTree
 
getModelManager() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Return a new model manager to create and keep track of entities
getModels(SecondaryDatabase, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getModels(HTable, Filter, TupleBinding, String, String, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getModels(HTable, Scan, Filter, TupleBinding, String, String, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getModels(String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getModelsByTag(SecondaryDatabase, TupleBinding, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getModelsByTag(String, HTable, HTable, TupleBinding, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getModelsByTag(String, String, String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getModelsTags(SecondaryDatabase, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
Get access to an iterator containing all the mismatch tags.
getModelsTags(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getModelsTags(String, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getModelsUnordered(Database, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
getModelsUnordered(String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
getModelTags(HTable) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
Other methods expect this to return a SeqWareIterator and not a HashMap.
getMODIFY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the modify property.
getModule() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SeqwareModuleJob
 
getModule() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusSeqwareModuleJob
 
getModuleArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getModuleType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getMostSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
getMULTIPLIER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Gets the value of the multiplier property.
getMutatedGenomicSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getMutatedTranslatedSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
getName() - Method in interface com.github.seqware.queryengine.model.AnalysisSet
Get the name of the analysisSet
getName() - Method in interface com.github.seqware.queryengine.model.Group
Get the name of the group
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet
 
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
 
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
 
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
getName() - Method in interface com.github.seqware.queryengine.model.Reference
The name of this reference (ex: "hg 19")
getName() - Method in interface com.github.seqware.queryengine.model.ReferenceSet
Get the name of the reference set
getName() - Method in interface com.github.seqware.queryengine.model.TagSet
Get the name of the tag set
getName() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getName() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getName() - Method in class net.sourceforge.seqware.common.model.IUS
 
getName() - Method in class net.sourceforge.seqware.common.model.Lane
 
getName() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
getName() - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
getName() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
getName() - Method in class net.sourceforge.seqware.common.model.Organism
 
getName() - Method in class net.sourceforge.seqware.common.model.Platform
 
getName() - Method in class net.sourceforge.seqware.common.model.Project
 
getName() - Method in class net.sourceforge.seqware.common.model.Sample
 
getName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getName() - Method in class net.sourceforge.seqware.common.model.StudyType
 
getName() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getName() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
if executable is not null && executable is not CUSTOM
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
 
getName() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module
 
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getName() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.WorkflowExecutable
 
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
getName() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the name property.
getName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Gets the value of the name property.
getName() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
getName() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getName() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
 
getName() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
getNameNode() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
 
getNamespace() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.WorkflowExecutable
 
getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
getNcbiTaxId() - Method in class net.sourceforge.seqware.common.model.Organism
 
getNcbiTaxonomyId() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
 
getNestedTags() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
getNestedTags() - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Get tags that have been sorted into a structure of Nested Maps.
getNetworkReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getNewStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
Gets the value of the newStudyType property.
getNewType() - Method in class net.sourceforge.seqware.common.model.Study
 
getNodeHtml(Processing, Registration, String, boolean, boolean, boolean, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getNodeHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getNodeIds(Object) - Static method in class net.sourceforge.solexatools.util.FindChildUtil
 
getNominalLength() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getNOMINALLENGTH() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Gets the value of the nominallength property.
getNominalSdev() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getNOMINALSDEV() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Gets the value of the nominalsdev property.
getNotes() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Gets the value of the notes property.
getNotRunned() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getNumber() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
getNumberChannels() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the numberChannels property.
getNUMBEROFLEVELS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Gets the value of the numberoflevels property.
getNUMBEROFREADSPERSPOT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Gets the value of the numberofreadsperspot property.
getNumQueries() - Method in interface com.github.seqware.queryengine.system.exporters.QueryDumperInterface
Return the number of queries that we wish to run consecutively
getOffspringProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
getOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getOrganism() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getOrganism() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
 
getOrganism() - Method in interface com.github.seqware.queryengine.model.ReferenceSet
Get the organism associated with this reference set
getOrganism() - Method in class net.sourceforge.seqware.common.model.Lane
 
getOrganism() - Method in class net.sourceforge.seqware.common.model.Sample
 
getOrganism() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getOrganismId() - Method in class net.sourceforge.seqware.common.model.Organism
 
getOrganismId() - Method in class net.sourceforge.seqware.common.model.Sample
 
getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
 
getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
getORIENTATION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Gets the value of the orientation property.
getOriginalFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
getOs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
getOutput() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
 
getOutputDir() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusSeqwareModuleJob
 
getOutputFilename() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
getOutputFilename() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
getOutputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
getOwner() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get the owner for the object
getOwner() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getOwner() - Method in class net.sourceforge.seqware.common.model.File
 
getOwner() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getOwner() - Method in class net.sourceforge.seqware.common.model.IUS
 
getOwner() - Method in class net.sourceforge.seqware.common.model.Lane
 
getOwner() - Method in class net.sourceforge.seqware.common.model.Processing
 
getOwner() - Method in class net.sourceforge.seqware.common.model.Sample
 
getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getOwner() - Method in class net.sourceforge.seqware.common.model.Study
 
getOwner() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getOwner() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getOwner() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getOwnerId() - Method in class net.sourceforge.seqware.common.model.Project
 
getOwnerSGID() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get the owner for the object
getPage() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
getPageInfo(HttpServletRequest, String, List, List, String, String, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
 
getPageInfoSD(HttpServletRequest, String, List, List, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
 
getPageNumber(HttpServletRequest, Study, List<Study>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
 
getPaidAmount() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getPAIRED() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
Gets the value of the paired property.
getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getPairedOrientation() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getParameters() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
getParameters() - Method in class com.github.seqware.queryengine.kernel.RPNStack
Returns the parameters of the argument stack, i.e., everything that is not a constant and considered to be a variable.
getParameters() - Method in class com.github.seqware.queryengine.model.Analysis
Get the parameters for this particular creation of an analysis plug-in
getParameters() - Method in class net.sourceforge.seqware.common.model.Processing
 
getParameters() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getParameters() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
getParams() - Method in class net.sourceforge.solexatools.util.SummaryLine
 
getPARENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the parent property.
getParentAccessionId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
getParentLane(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
getParentProcessing(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
getParentProcessingAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
getParentProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
getParents() - Method in class net.sourceforge.seqware.common.model.Processing
 
getParents() - Method in class net.sourceforge.seqware.common.model.Sample
 
getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
getParentUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getParentWorkflowAccessions() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getPassword() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getPassword() - Method in class com.github.seqware.queryengine.model.User
A hashed password for the user
getPassword() - Method in class net.sourceforge.seqware.common.model.Registration
 
getPassword() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getPasswordHint() - Method in class net.sourceforge.seqware.common.model.Registration
 
getPathToFirstFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getPathToSecondFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getPending() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getPermanentBundleLocation() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getPermBundleLocation() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getPermissions() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
getPermissions() - Method in interface com.github.seqware.queryengine.model.interfaces.ACLable
Get permissions for the subject.
getPfn() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
getPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getPhase() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getPhase() - Method in class com.github.seqware.queryengine.model.Feature
(GVF: The phase column is not used in GVF, but is maintained with the placeholder '.' (period) for compatibility with GFF3 and tools that conform to the GFF3 specification (and do change it))
getPlatform() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getPLATFORM() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the platform property.
getPlatformId() - Method in class net.sourceforge.seqware.common.model.Platform
 
getPlatformInt() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getPlatformInt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getPlatformService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
 
getPlatformServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getPlugin() - Method in class com.github.seqware.queryengine.model.Analysis
Get analysis plugin
getPlugin() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
 
getPmi() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getPmi() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getPostgresqlPersistenceStrategy() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getPragma() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getPragma() - Method in class com.github.seqware.queryengine.model.Feature
GVF provides pragmas that are file-wide.
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getPrecedingIDBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getPrecedingIDBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getPrecedingIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getPrecedingIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getPrecedingSGID() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Used in back-end to get previous version ID
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable
Returns the subject (if any) that represents a previous version.
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getPredicate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getPredicate() - Method in class com.github.seqware.queryengine.model.Tag
Get the predicate.
getPreJobDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getPricePerUnit() - Method in class net.sourceforge.seqware.common.model.Expense
 
getPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getProcessedCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
getProcessedCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.Lane
 
getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getProcessedCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getProcessExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing
 
getProcessExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
getProcessing() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
getPROCESSING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the processing property.
getProcessingAccession() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
getProcessingAttributeId() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
getProcessingAttributes() - Method in class net.sourceforge.seqware.common.model.Processing
 
getProcessingByChildId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
 
getProcessingByParentId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
 
getProcessingCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
getProcessingCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.Lane
 
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getProcessingCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getProcessingExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getProcessingExperimentsId() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
getProcessingExperimentsService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getProcessingHtml(Processing, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getProcessingId() - Method in class net.sourceforge.seqware.common.model.Processing
 
getProcessingIusId() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
getProcessingIusService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getProcessingIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getProcessingLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getProcessingLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getProcessingLanesId() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
getProcessingRelationshipId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
 
getProcessingRelationshipService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getProcessingRelationshipServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.File
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.IUS
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.Lane
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.Sample
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.Study
 
getProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getProcessingSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getProcessingSamplesId() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
getProcessingSamplesService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getProcessingsByWorkflow(WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
 
getProcessingSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getProcessingSequencerRunsId() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
getProcessingSequencerRunsServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getProcessingService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
getProcessingServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getProcessingStudiesId() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
getProcessingStudiesService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getProcessingStudiesServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getProcStatuses(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
getProcStatuses(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
getProfiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getProjectId() - Method in class net.sourceforge.seqware.common.model.Project
 
getProjectId() - Method in class net.sourceforge.seqware.common.model.Study
 
getPROJECTID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the projectid property.
getProperties() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getProperty(String) - Static method in class com.github.seqware.queryengine.common.ConfigTools
 
getProperty(String) - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
 
getProperty(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getProperty(String) - Static method in class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil
 
getPROTECT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the protect property.
getPublic() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getQCREPORT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the qcreport property.
getQtype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Gets the value of the qtype property.
getQualityMultiplier() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getQualityNumberOfLevels() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getQualityScorer() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getQUALITYSCORER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Gets the value of the qualityscorer property.
getQUALITYSCORES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
Gets the value of the qualityscores property.
getQualityType() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getQuery(FeatureSet, int) - Method in interface com.github.seqware.queryengine.system.exporters.QueryDumperInterface
Return each of the getNumQueries
getQueryInterface() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Get a reference to the currently operating Query Interface
getQueue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getReadBases() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReadClass() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getREADCLASS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the readclass property.
getReadCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReader() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
 
getReadIndex() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getREADINDEX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the readindex property.
getReadLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getReadSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
getREADSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Gets the value of the readspec property.
getReadSpecs() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
getReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
getReadsSupportingCallOne() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReadsSupportingCallThree() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReadsSupportingCallTwo() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReadType() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
getREADTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the readtype property.
getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getReference() - Method in class com.github.seqware.queryengine.model.FeatureSet
Get the reference for this featureSet
getReference() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Get the reference for this featureSet
getReference() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Get the reference for this featureSet
getREFERENCEALIGNMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the referencealignment property.
getReferenceAveSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReferenceBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReferenceCallQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getReferenceID() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getReferenceID() - Method in class com.github.seqware.queryengine.model.FeatureSet
Get the referenceID for the associated reference
getReferenceID() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
getReferenceID() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
getReferenceId() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getReferenceIDBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getReferenceIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getReferenceIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getReferenceIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceMaxSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getReferenceName() - Method in class com.github.seqware.queryengine.util.FSGID
 
getReferences() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
getReferences() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getReferences() - Method in interface com.github.seqware.queryengine.model.QueryInterface
 
getReferences(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getReferenceSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
getReferenceSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getReferenceSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface
 
getReferenceSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getRefName() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
Gets the value of the refname property.
getRegion() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the region property.
getRegions() - Method in class net.sourceforge.seqware.common.model.Lane
 
getRegions() - Method in class net.sourceforge.seqware.common.model.Sample
 
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareFile
 
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareLane
 
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareSample
 
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
getRegistration(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security
 
getRegistrationId() - Method in class net.sourceforge.seqware.common.model.Registration
 
getRegistrationService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
 
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
 
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
 
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
 
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
 
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
 
getRegistrationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getRelationship() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
 
getRelativeLocation() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getRELEASE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the release property.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService
 
getReportForSequencerRun(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.FileReportService
 
getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService
 
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
getReportForSequencerRun(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
 
getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
 
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
getReportForSequencerRuns(String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
 
getReportForSequencerRuns(String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService
 
getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService
 
getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
 
getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
 
getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
getRepresentation(Document) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
 
getRequestedTypeList(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
 
getRequestedTypeList(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
getResourceInfo(ApplicationInfo) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
 
getReturnValue() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
 
getReturnValue() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getReturnValues() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
getRights(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getRights(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getRights(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getRightsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getRightsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getRightsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getRightsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getRightsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getRightsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getRootProcessing(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
getRootProcessing(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
getRootProcessing(WorkflowRun) - Static method in class net.sourceforge.solexatools.util.FindChildUtil
 
getRootProcessingName() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getRootProcessingSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getRootSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
getRootSample(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
getRootSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
getRootSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
getRootSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
getRowId() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getRowId() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
getRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getRowKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getRowKey() - Method in class com.github.seqware.queryengine.util.FSGID
Get the HBase-style row-key for this Feature
getRowKey() - Method in class com.github.seqware.queryengine.util.SGID
Output the portion of the SGID that is used as a rowKey
getRows() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getRUN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunSet
Gets the value of the run property.
getRUNATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES
Gets the value of the runattribute property.
getRUNATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runattributes property.
getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getRunCenter() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runCenter property.
getRunDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runDate property.
getRunFile() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runFile property.
getRUNLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS
Gets the value of the runlink property.
getRUNLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runlinks property.
getRunName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getRunningCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
getRunningCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
getRUNREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the runref property.
getRunsFromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Using a workflow SWID, find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.
getRunStartTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
 
getRunStartTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getRunStopTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
 
getRunStopTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getRunSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getS3InputStream(String, int, long, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
getS3InputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
getS3Url(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
getS3Url(String, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
getSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getSample() - Method in class net.sourceforge.seqware.common.model.IUS
 
getSample() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSample() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
getSample() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
getSample() - Method in class net.sourceforge.seqware.common.model.SampleLink
 
getSample() - Method in class net.sourceforge.seqware.common.model.SampleSearch
 
getSample() - Method in class net.sourceforge.seqware.common.model.ShareSample
 
getSample() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getSample() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getSAMPLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleSet
Gets the value of the sample property.
getSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getSample_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getSAMPLEATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES
Gets the value of the sampleattribute property.
getSampleAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
getSampleAttributes() - Method in class net.sourceforge.seqware.common.model.Sample
 
getSAMPLEATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the sampleattributes property.
getSampleCode() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSAMPLEDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Gets the value of the sampledescriptor property.
getSampleHtml(Sample, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getSampleHtml(Sample, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getSampleId() - Method in class net.sourceforge.seqware.common.model.Sample
 
getSampleId() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
Gets the value of the sampleId property.
getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Gets the value of the sampleId property.
getSampleId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
 
getSAMPLELINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS
Gets the value of the samplelink property.
getSampleLinkId() - Method in class net.sourceforge.seqware.common.model.SampleLink
 
getSampleLinks() - Method in class net.sourceforge.seqware.common.model.Sample
 
getSAMPLELINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the samplelinks property.
getSampleName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getSAMPLENAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the samplename property.
getSAMPLEPOOLREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the samplepoolref property.
getSAMPLEREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the sampleref property.
getSampleRef() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
Gets the value of the sampleRef property.
getSampleRef() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Gets the value of the sampleRef property.
getSampleReportService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getSampleReportServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getSamples() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getSamples() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSamples() - Method in class net.sourceforge.seqware.common.model.Processing
 
getSamples() - Method in class net.sourceforge.seqware.common.model.Project
 
getSamples() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getSampleSearch() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
getSampleSearchAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
getSampleSearchAttributes() - Method in class net.sourceforge.seqware.common.model.SampleSearch
 
getSampleSearchId() - Method in class net.sourceforge.seqware.common.model.SampleSearch
 
getSampleSearchService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getSampleSearchServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getSampleService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getSampleService() - Method in class net.sourceforge.solexatools.validation.SampleValidator
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
 
getSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getSampleSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getSampleSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getSampleType() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSampleUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
 
getSchema() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Gets the value of the schema property.
getSchema() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Gets the value of the schema property.
getScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getScore() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getScore() - Method in class com.github.seqware.queryengine.model.Feature
(GVF: The score of the feature, an integer or floating point number.)
getScore() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getSector() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the sector property.
getSelectedIds(HttpServletRequest, String, String[], String[]) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
getSelectedWorkflowParamValue(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
getSelection() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getSender() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
 
getSeqid() - Method in class com.github.seqware.queryengine.model.Feature
User provided ID for the feature (GVF: The chromosome or contig on which the sequence_alteration is located (text).)
getSequenceOntologyAccession(String) - Static method in class com.github.seqware.queryengine.kernel.Compression
 
getSequenceOntologyAccessionSurrogate(String) - Static method in class com.github.seqware.queryengine.kernel.Compression
Returns the compressed surrogate for a particular SO accession.
getSequencer_run_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
getSequencerRun(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
 
getSequencerRun(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
 
getSequencerRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
 
getSequencerRunAttributeId() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
getSequencerRunAttributes() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSequencerRunHtml(SequencerRun, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getSequencerRunReport() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
FIXME: this is a hack, will need to add an object layer between this metadata object and the response
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getSequencerRunReportIds(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getSequencerRunReportIds(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getSequencerRuns() - Method in class net.sourceforge.seqware.common.model.Processing
 
getSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
 
getSequencerRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getSequencerRunSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getSequencerRunValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
getSequencerRunWizardDTO() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
getSequencerRunWizardValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
getSequencers() - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
getSequencers(int) - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
getSequencers() - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
getSequencers(int) - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
getSequencers() - Static method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
getSequencers(int) - Static method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
getSequenceSpace() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getSEQUENCESPACE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
Gets the value of the sequencespace property.
getSEQUENCINGPROTOCOL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the sequencingprotocol property.
getSeqwareRevision() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getSeqwareVersion() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getSerialization() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Get a reference to the current operating serialization method
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.ApacheSerialization
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.KryoSerialization
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization
 
getSerializationConstant() - Method in interface com.github.seqware.queryengine.impl.SerializationInterface
Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Experiment
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Lane
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Platform
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Processing
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Project
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Sample
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Study
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.StudyType
 
getServer() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getSessionFactory() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getSessionFactoryBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getSettings() - Static method in class com.github.seqware.queryengine.common.ConfigTools
The output keys are always uppercase!
getSettings() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
The output keys are always uppercase!
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.factory.Factory
 
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.factory.FactoryInterface
 
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
getSETTINGS_MAP() - Static method in class com.github.seqware.queryengine.Constants
Get the settings map.
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getSGID() - Method in interface com.github.seqware.queryengine.model.Atom
Get the universally unique identifier of this object.
getSGID() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the universally unique identifier of this object.
getSGID() - Method in class com.github.seqware.queryengine.util.LazyReference
Get the underlying SGID for the lazy reference
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getSharedStudies() - Method in class net.sourceforge.seqware.common.model.Study
 
getSharedWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getShareExperimentId() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
getShareFileId() - Method in class net.sourceforge.seqware.common.model.ShareFile
 
getShareLaneId() - Method in class net.sourceforge.seqware.common.model.ShareLane
 
getShareProcessingId() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
getShareSampleId() - Method in class net.sourceforge.seqware.common.model.ShareSample
 
getShareStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
getShareWorkflowRun(String, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
 
getShareWorkflowRun(String, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
getShareWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
 
getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
getSINGLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
Gets the value of the single property.
getSingleWorkflowRun(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Using a workflow run SWID, report on the files, samples and processing events associated with the run.
getSite() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Pfn
 
getSize() - Method in class net.sourceforge.seqware.common.model.File
 
getSize() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
getSkip() - Method in class net.sourceforge.seqware.common.model.IUS
 
getSkip() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSkip() - Method in class net.sourceforge.seqware.common.model.Sample
 
getSkip() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSkip() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getSkipTxt() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getSortKeySample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getSource() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getSource() - Method in class com.github.seqware.queryengine.model.Feature
(GVF: The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature.)
getSource() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getSource() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Gets the value of the source property.
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Gets the value of the source property.
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Gets the value of the source property.
getSourceReader(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
This attempts to resume if passed in startPosition > 0.
getSPOTDECODEMETHOD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
Gets the value of the spotdecodemethod property.
getSPOTDECODESPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
Gets the value of the spotdecodespec property.
getSPOTDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Gets the value of the spotdescriptor property.
getSpotDesignReadSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getSql() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getStart() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getStart() - Method in class com.github.seqware.queryengine.model.Feature
Start coordinate, 0-based (GVF: 1-based integer for the beginning of the sequence_alteration locus on the plus strand (integer))
getStart() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
getStartDate() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getStartPage() - Method in class net.sourceforge.solexatools.util.PageInfo
 
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
 
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getState(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Accessor method for the back-end.
getState() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
getState(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
getState() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getStats() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getStatus() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getStatus() - Method in class net.sourceforge.seqware.common.model.Processing
 
getStatus() - Method in class net.sourceforge.seqware.common.model.Project
 
getStatus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getStatus() - Method in class net.sourceforge.seqware.common.model.Study
 
getStatus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getStatus() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
 
getStatusCmd() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getStatusCount(Study, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
getStatusCount(Study, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
getStatusCounts() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
getStatuses() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getStderr() - Method in class net.sourceforge.seqware.common.model.Processing
 
getStdErr() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getStderr() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getStderrFile() - Method in class net.sourceforge.seqware.pipeline.module.Module
Getter for the file where the stderr will be redirected.
getStdout() - Method in class net.sourceforge.seqware.common.model.Processing
 
getStdOut() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getStdout() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getStdoutFile() - Method in class net.sourceforge.seqware.pipeline.module.Module
Getter for the file where the stdout will be redirected.
getStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getStop() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getStop() - Method in class com.github.seqware.queryengine.model.Feature
Stop coordinate, 0-based (GVF: 1-based integer of the end of the sequence_alteration on plus strand (integer).)
getStop() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
 
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getStorage() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Get a reference to the currently operating storage method
getStore(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.factory.Factory
 
getStore(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.factory.FactoryInterface
 
getStore(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.factory.impl.BerkeleyDBFactory
 
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
getStore(String, Long, int) - Static method in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
 
getStoreType() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getStrand() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getStrand() - Method in class com.github.seqware.queryengine.model.Feature
Strand of the feature.
getStrand() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getStrand() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getStrategy() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
getStrExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getStrExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getStrExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample
 
getStrExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample
 
getStrLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
 
getStrRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getStrStartURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getStrStartURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getStudies() - Method in class net.sourceforge.seqware.common.model.Processing
 
getStudy() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getStudy() - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
getStudy() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
getStudy() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
getStudy() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
getStudy() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
getStudy() - Method in class net.sourceforge.seqware.common.model.StudyLink
 
getSTUDY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudySet
Gets the value of the study property.
getStudy(Experiment) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
 
getStudy(Sample) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
 
getStudy(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
 
getStudy(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
 
getSTUDYABSTRACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the studyabstract property.
getSTUDYATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES
Gets the value of the studyattribute property.
getStudyAttributeId() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
getStudyAttributes() - Method in class net.sourceforge.seqware.common.model.Study
 
getSTUDYATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the studyattributes property.
getStudyDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
getSTUDYDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the studydescription property.
getStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
getStudyId() - Method in class net.sourceforge.seqware.common.model.Study
 
getSTUDYLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS
Gets the value of the studylink property.
getStudyLinkId() - Method in class net.sourceforge.seqware.common.model.StudyLink
 
getStudyLinks() - Method in class net.sourceforge.seqware.common.model.Study
 
getSTUDYLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the studylinks property.
getSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the studyref property.
getSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the studyref property.
getStudyService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getStudyService() - Method in class net.sourceforge.solexatools.validation.StudyValidator
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
getStudyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getStudySwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getSTUDYTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the studytitle property.
getSTUDYTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the studytype property.
getStudyTypeDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
getStudyTypeId() - Method in class net.sourceforge.seqware.common.model.StudyType
 
getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
 
getStydyHtml(Study, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getStydyHtml(Study, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
getSubject(String, String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos
 
getSubjectEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
 
getSUBMISSION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet
Gets the value of the submission property.
getSubmissionComment() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the submissionComment property.
getSubmissionDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the submissionDate property.
getSubmissionId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the submissionId property.
getSum() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
getSummaryData(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
getSummaryLines() - Method in class net.sourceforge.solexatools.util.SummaryData
 
getSUPPRESS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the suppress property.
getSvType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getSwa() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Expense
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.File
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Invoice
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.IUS
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Processing
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Sample
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareFile
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareLane
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareSample
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Study
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getSwAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getSynonymMap() - Method in class com.github.seqware.queryengine.util.obo.OboParser
Hacked map of terms to synonyms
getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup
 
getSyntax() - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
 
getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner
 
getTablename() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
getTablename() - Method in class com.github.seqware.queryengine.util.FSGID
 
getTag() - Method in interface net.sourceforge.seqware.common.model.Attribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.IUS
 
getTag() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
getTag() - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag
 
getTag(Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Gets the value of the tag property.
getTagByKey(String) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
getTagByKey(String) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Quickly get the value of a tag by the key.
getTagMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getTagMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTags(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTags(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTags() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
getTags() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getTags() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
getTags() - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Get tags that the implementing class has been tagged with
getTags() - Method in interface com.github.seqware.queryengine.model.QueryInterface
 
getTags() - Method in class com.github.seqware.queryengine.model.Tag
Tags are not taggable, but it is actually easier to have the capability via inheritance and just turn it off
getTags() - Method in class net.sourceforge.seqware.common.model.Lane
 
getTags() - Method in class net.sourceforge.seqware.common.model.Sample
 
getTags() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
 
getTags() - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface
 
getTags() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getTags(Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getTags(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTagsCount() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTagsCount() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getTagSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getTagSet() - Method in class com.github.seqware.queryengine.model.Tag
Get a reference to the parent TagSet
getTagSetBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getTagSetIDs() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getTagSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getTagSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getTagSetOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagHierarchicalOccurrence
 
getTagSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
getTagSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getTagSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface
 
getTagSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getTagSetSGID() - Method in class com.github.seqware.queryengine.model.Tag
Get a reference to the parent TagSet
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTagsList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTagsList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTagsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTagsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTagsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTagsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTagSpec(String) - Method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
Given a key, locate a potential match inside a list of tag sets, otherwise create a new one in the ad hoc set.
getTagSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
getTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagSpecIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagSpecIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagSpecIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagSpecIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getTagValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
Gets the value of the target property.
getTAXONID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Gets the value of the taxonid property.
getTemplate() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getTemplate() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getTemplateEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
 
getTemplateFile() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
getTemplatePath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getTemplateType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
getTerm_name() - Method in enum com.github.seqware.queryengine.Constants.Term
 
getTermValue(Class<T>) - Method in enum com.github.seqware.queryengine.Constants.Term
 
getTest() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getTestCmd() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getThickEnd() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getThickStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getThreadCount() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getTimestamp() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
getTimestamp() - Method in interface com.github.seqware.queryengine.model.Atom
Get a creation time for this resource.
getTimestamp() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get a creation time for this resource.
getTimeTaken() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
getTissSource() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
getTitle() - Method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
 
getTitle() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getTitle() - Method in class net.sourceforge.seqware.common.model.Sample
 
getTitle() - Method in class net.sourceforge.seqware.common.model.Study
 
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the title property.
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the title property.
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the title property.
getTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getTombstone() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getTotal() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
getTotalDataBlocks() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the totalDataBlocks property.
getTotalPrice() - Method in class net.sourceforge.seqware.common.model.Expense
 
getTotalReads() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the totalReads property.
getTotalSpots() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the totalSpots property.
getTotalUnits() - Method in class net.sourceforge.seqware.common.model.Expense
 
getTRANSCRIPTASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the transcriptassembly property.
getTranscriptId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
getTRANSCRIPTSEQUENCING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the transcriptsequencing property.
getTranslatedSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
getTranslocationDestinationContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getTranslocationDestinationStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getTranslocationDestinationStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getTranslocationType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getTTL() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
getTTL() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return the expiry date in terms of hours in the future (may fail if the time difference is too large)
getType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getType() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getType() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
getType() - Method in class com.github.seqware.queryengine.model.Feature
(From GVF: The type of the feature, this is constrained to be either: (a) the SO term sequence_alteration (SO:0001059), (b) a child term of sequence_alteration, (c) the SO term gap (SO:0000730), or (d) the SO accession number for any of the previous terms.)
getType() - Method in class net.sourceforge.seqware.common.model.File
 
getType() - Method in class net.sourceforge.seqware.common.model.Sample
 
getType() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getType() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
getType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
getType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
getType() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
 
getTypeNode() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getUids(NamingEnumeration<SearchResult>) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
 
getUniqueName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
getUniqueName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
getUnit() - Method in interface net.sourceforge.seqware.common.model.Attribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
getUnit() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
getUnits() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
getUnits() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
getUnits() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
getUnits() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
getUnits() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
getUnits() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
getUnits() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Gets the value of the units property.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Project
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile
 
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane
 
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample
 
getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
getUrl() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
getUrl() - Method in class net.sourceforge.seqware.common.model.File
 
getUrl() - Method in class net.sourceforge.seqware.common.model.IUSLink
 
getUrl() - Method in class net.sourceforge.seqware.common.model.LaneLink
 
getUrl() - Method in class net.sourceforge.seqware.common.model.Processing
 
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
getUrl() - Method in class net.sourceforge.seqware.common.model.SampleLink
 
getUrl() - Method in class net.sourceforge.seqware.common.model.StudyLink
 
getUrl() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getUrl() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getUrl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Pfn
 
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
Gets the value of the url property.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
 
getUrlLabel() - Method in class net.sourceforge.seqware.common.model.File
 
getUrlLabel() - Method in class net.sourceforge.seqware.common.model.Processing
 
getUrlLabel() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getUrlLabel() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
Gets the value of the urllink property.
getUrlString() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
getUseOneURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getUser() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getUserBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getUsername() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getUsername() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
getUserOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getUserOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getUserOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsers(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUsers() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
getUsers() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getUsers() - Method in interface com.github.seqware.queryengine.model.QueryInterface
Gets all users in all groups
getUsers() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getUsersBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsersCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUsersList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsersList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUsersOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsersOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUsersOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsersOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUseTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
getUseURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
 
getUuid() - Method in class com.github.seqware.queryengine.util.SGID
Get underlying UUID implementation, should only be called within the back-end
getVALIDATE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the validate property.
getValidationReportService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.FileController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
 
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
 
getValue() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Constant
 
getValue() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
getValue() - Method in class com.github.seqware.queryengine.model.Tag
Get the value.
getValue() - Method in interface net.sourceforge.seqware.common.model.Attribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
 
getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
 
getValue() - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag
 
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Gets the value of the value property.
getValue() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Gets the value of the value property.
getValue() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
getValueDescriptor() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
getValues() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVBytes() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVDouble() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVersion() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
getVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
getVersion() - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable
Get version for the subject
getVersion() - Method in interface com.github.seqware.queryengine.model.QueryInterface
 
getVersion() - Method in class net.sourceforge.seqware.common.model.Processing
 
getVersion() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getVersion() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
getVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getVersion() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.WorkflowExecutable
 
getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
getVersion() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
getVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVFloat() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getViewName(String) - Static method in class net.sourceforge.solexatools.util.Constant
 
getVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVInteger() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVisibleParams() - Method in class net.sourceforge.solexatools.util.SummaryData
 
getVisibleWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getVisibleWorkflowParamsWithDifferentValue() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVLong() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVSGIDRef() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVSGIDRefBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVSGIDRefOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVSGIDRefOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVSGIDRefOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVString() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getvType() - Method in class com.github.seqware.queryengine.model.Tag
Get the type of value for the tag value
getWfRuns() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
getWidth() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
getWorkerName() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
getWorkerName() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
getWorkflow() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusAbstract
 
getWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowContext
 
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowAccession(String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowAccession() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getWorkflowAccession() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getWorkflowAccession(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getWorkflowAccessionsToCheck() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getWorkflowAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
getWorkflowAttributes() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getWorkflowDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getWorkflowId() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getWorkflowInfo() - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
 
getWorkflowMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getWorkflowParam() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
getWorkflowParamMetadata(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getWorkflowParamService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
 
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
 
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
 
getWorkflowParamServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getWorkflowParamsWithDifferentFileMetaType() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getWorkflowParamValueId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
getWorkflowParamValueService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
 
getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
 
getWorkflowParamValueServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getWorkflowProperty(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusAbstract
 
getWorkflowRun() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRun(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Expense
 
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Processing
 
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
getWorkflowRunAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
getWorkflowRunAttributes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getWorkflowRunByAncestorWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing
 
getWorkflowRunHtml(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getWorkflowRunHtmlWithIUSs(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing
 
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getWorkflowRunInfo(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
getWorkflowRunParam(SortedSet<WorkflowParam>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
getWorkflowRunParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
getWorkflowRunParams() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getWorkflowRunProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunReport(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowRunReport(int, Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowRunReport(Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.IUS
 
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Lane
 
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunsByHost(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunsByStatus(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
 
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
 
getWorkflowRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunWithWorkflow(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getWorkflowsAndRuns() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getWorkflowService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
 
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
 
getWorkflowServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
 
getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
 
getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
 
getWorkflowSqwVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getWorkflowsRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
 
getWorkflowState(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
This method examines a Pegasus log directory using the status command provided and will encode the state of the workflow in the ReturnValue object, running as ReturnValue.PROCESSING, failed as ReturnValue.FAILURE, and success as ReturnValue.SUCCESS.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
 
getXML() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
 
getXREFLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Gets the value of the xreflink property.
getZygosity() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
GFF3_DELETION - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GFF3_INSERTION - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GFF3_SNV - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GFF3_UNKNOWN_TYPE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GFF3VariantImportWorker - Class in com.github.seqware.queryengine.system.importers.workers
Ported GFF3VariantImportWorker now using our Hibernate-like entry.
GFF3VariantImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.GFF3VariantImportWorker
 
GFF3VariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
GFF3VariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.GFF3VariantImportWorker
 
GITest - Class in com.github.seqware.queryengine.tutorial
This is a quick and sample application built on top of our API, created for Poster testing.
GITest(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.GITest
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Expense
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.File
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.IUS
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Lane
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Processing
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Registration
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Sample
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Study
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
givesPermission(Registration) - Method in interface net.sourceforge.seqware.common.security.PermissionsAware
 
grabFeatureListsGivenRow(Result, SGID, SerializationInterface) - Static method in class com.github.seqware.queryengine.impl.HBaseStorage
 
grabObjectsToBeFlushed() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
Group - Interface in com.github.seqware.queryengine.model
A Group of users that may share ACL permissions
group - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
Group.Builder - Class in com.github.seqware.queryengine.model
 
Group.Builder() - Constructor for class com.github.seqware.queryengine.model.Group.Builder
 
GroupIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
GroupIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.GroupIO
 
GRP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
GRPS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
GVF_ALIAS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_BREAKPOINT_DETAIL - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_DBXREF - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_END_RANGE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_GENOTYPE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_HEMIZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_HETEROZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_HOMOZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_INDIVIDUAL - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_PHASED - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_REFERENCE_AA - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_REFERENCE_CODON - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_REFERENCE_SEQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_SEQUENCE_CONTEXT - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_START_RANGE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_TOTAL_READS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_VARIANT_AA - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_VARIANT_CODON - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_VARIANT_EFFECT - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_VARIANT_FREQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_VARIANT_READS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_VARIANT_SEQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
GVF_ZYGOSITY - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 

H

handle(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
 
handle(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
 
handle - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource
 
handle(Callback[]) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler
 
handleAtom2PB(QESupporting.AtomPB, AtomImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Handle serialization of the core atom
handleAtom2PB(QESupporting.FeatureAtomPB, Feature) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Handle serialization of the core atom just for Features
handleCancel(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Handles the user's request to delete their study.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to cancel the lane or the lane update page.
handleCancel(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
Handles the user's request to cancel.
handleCancel(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to cancel the lane or the lane update page.
handleCancel(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to cancel the sequencerRun or the sequencerRun update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Handles the user's request to cancel the registration or the registration update page.
handleCancel(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Handles the user's request to cancel the experiment or the experiment update page.
handleCancel(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Handles the user's request to cancel the experiment or the experiment update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to cancel the registration or the registration update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Handles the user's request to cancel the registration or the registration update page.
handleCompressedInput(String) - Static method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
 
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to delete their experiment.
handleDelete(HttpServletRequest, HttpServletResponse, File) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to delete their file.
handleDelete(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
Handles the user's request to delete their ius.
handleDelete(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to delete their lane.
handleDelete(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to delete their processing.
handleDelete(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to delete their sample.
handleDelete(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to delete their study.
handleDeserialization(byte[]) - Static method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBaseBatchedPlugin
 
handleDeserialization(byte[]) - Static method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin
 
handleGroupByAttribute(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
handleMol2PB(QueryEngine.MoleculePB, MoleculeImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
This should handle serialization of molecule
handleNext(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
Handles the user's request to submit a new study.
handleNext(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Handles the user's request to submit a new study.
handlePB2Atom(QESupporting.AtomPB, AtomImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Handle de-serialization of the core atom
handlePB2Atom(QESupporting.FeatureAtomPB, Feature) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Handle de-serialization of the core atom just for Features FIXME: this should be collapsible with normal atom
handlePB2Mol(QueryEngine.MoleculePB, MoleculeImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
This should handle de-serialization of molecule
handlePrevious(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
Handles the user's request to cancel the study or the study update page.
handlePrevious(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Handles the user's request to cancel the study or the study update page.
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LogoutController
Handles a user's logout request.
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
 
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
 
handleReset(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to reset the lane page during a new or update lane.
handleReset(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to reset the lane page during a new or update lane.
handleReset(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to reset the sequencerRun page during a new or update sequencerRun.
handleReset(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Handles the user's request to reset the registration page during a new or update registration.
handleReset(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to reset the sample page during a new or update sample.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to reset the registration page during a new or update registration.
handleReset(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Handles the user's request to reset the registration page during a new or update registration.
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBaseBatchedPlugin
 
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
Handle serialization of parameters.
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin
 
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin
 
handleShare(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Handles the user's request to share their WorkflowRun.
handleShare(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to share their study.
handleShare(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to share their study.
handleSubmit(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to submit a new lane.
handleSubmit(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to submit a new lane.
handleSubmit(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to submit a new sequencerRun.
handleSubmit(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Handles the user's request to submit a new registration.
handleSubmit(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Handles the user's request to submit a new experiment.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Handles the user's request to submit a new experiment.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to submit a new registration.
handleSubmit(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, UploadFile) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, UploadSequence) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Handles the user's request to submit a new registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to update their lane.
handleUpdate(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
Handles the user's request to delete their ius.
handleUpdate(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to update their lane.
handleUpdate(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to update their sequencerRun.
handleUpdate(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Handles the user's request to update their registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Handles the user's request to update their experiment.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Handles the user's request to update their experiment.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to update their registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Handles the user's request to update their registration.
hasAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
hasAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
hasAcl() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
hasCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
hasCascade() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
hasCommandOutput() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
hasDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
hasDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasEmailAddress() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasEmailAddressBeenUsed(String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
Determines if an email address has already been used.
hasEmailAddressBeenUsed(String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
 
hasExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
hasExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
hasExpiryTime() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
hasFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasFeatureSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasFirstName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
hasFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
hasFriendlyRowkey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
hasGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
hasGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
hasGrp() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
hashCode() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
hashCode() - Method in class com.github.seqware.queryengine.model.Feature
 
hashCode() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
hashCode() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
 
hashCode() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
hashCode() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
hashCode() - Method in class com.github.seqware.queryengine.model.Tag
 
hashCode() - Method in class com.github.seqware.queryengine.model.User
 
hashCode() - Method in class com.github.seqware.queryengine.util.LazyReference
 
hashCode() - Method in class com.github.seqware.queryengine.util.SGID
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Expense
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Experiment
 
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
hashCode() - Method in class net.sourceforge.seqware.common.model.File
 
hashCode() - Method in class net.sourceforge.seqware.common.model.FileType
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Invoice
 
hashCode() - Method in class net.sourceforge.seqware.common.model.IUS
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Lane
 
hashCode() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
hashCode() - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
hashCode() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Organism
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Platform
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Processing
 
hashCode() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Project
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Registration
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Sample
 
hashCode() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
hashCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
hashCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
hashCode() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
hashCode() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Study
 
hashCode() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
hashCode() - Method in class net.sourceforge.seqware.common.model.StudyType
 
hashCode() - Method in class net.sourceforge.seqware.common.model.Workflow
 
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
 
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
hasId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasId() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasLastName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
hasLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
hasLeastSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
hasMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
hasMostSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Determines if an email address has already been used.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
Determines if an email address has already been used.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Determines if an email address has already been used.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Determines if an email address has already been used.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
hasNext() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
 
hasNext() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
 
hasNext() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
 
hasNext() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
 
hasNext() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Super method for dealing with database iterator specifics, such as closing the DB-iterator when no more data is available.
hasNext() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
 
hasNextImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator
 
hasNextImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Implementation of hasNext().
hasOption(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Arguments
 
hasOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasOrganism() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
hasParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
hasParameters() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
hasPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasPassword() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasPhase() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasPragma() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
hasPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
hasPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasPredicate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasProcessingFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
hasProcessingFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
hasProvisionFilesDependent() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
hasProvisionFilesDependent() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusSeqwareModuleJob
 
hasReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasReferenceID() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasRefName() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasRowKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasScore() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
hasSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
hasSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasSource() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasStart() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasStop() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasStrand() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasTagSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
hasTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
hasTimestamp() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
hasTitleBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
hasTitleBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
Determines if an email address has already been used.
hasTitleBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Determines if an email address has already been used.
hasTitleBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
hasTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasTombstone() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasType() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
hasUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
hasUser() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
hasVariable(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.StringUtils
 
hasVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVBytes() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVDouble() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVFloat() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVInteger() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVLong() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVSGIDRef() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVString() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
HBaseModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
FIXME: need to create a locatable model iterator and then pass in the end point, otherwise the code that uses this object will need to do bounds checking!
HBaseModelIterator(ResultScanner, HTable, TupleBinding, String, String, boolean) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
 
HBaseModelManager - Class in com.github.seqware.queryengine.impl
A Simple implementation of the CreateUpdateManager interface.
HBaseModelManager() - Constructor for class com.github.seqware.queryengine.impl.HBaseModelManager
 
HBasePersistentBackEnd - Class in com.github.seqware.queryengine.impl
Implement HBase optimizations for the back-end
HBasePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
 
HBaseRead2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
 
HBaseRead2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseRead2
 
HBaseReadWriteExample - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
 
HBaseReadWriteExample() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseReadWriteExample
 
HBaseStorage - Class in com.github.seqware.queryengine.impl
 
HBaseStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage
 
HBaseStorage.FeatureScanIterable - Class in com.github.seqware.queryengine.impl
A scanner specifically for Features.
HBaseStorage.FeatureScanIterable(ResultScanner, SGID) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterable
 
HBaseStorage.FeatureScanIterator - Class in com.github.seqware.queryengine.impl
Presents an interface for iterating through FeatureLists
HBaseStorage.FeatureScanIterator(ResultScanner, SGID) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
 
HBaseStorage.ScanIterable - Class in com.github.seqware.queryengine.impl
A generic scanner
HBaseStorage.ScanIterable(ResultScanner, Class) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
 
HBaseStorage.ScanIterator - Class in com.github.seqware.queryengine.impl
Presents an interface for iterating through SGIDs
HBaseStorage.ScanIterator(ResultScanner, Class) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
 
HBaseStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl
 
HBaseStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
HBaseTagModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
 
HBaseTagModelIterator(String, ResultScanner, HTable, TupleBinding, String, String) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
 
helicos - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource
 
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource
 
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource
 
HelloWorld - Class in net.sourceforge.seqware.pipeline.modules.examples
This is a hello world module that should give you an idea of how to create a module of your own.
HelloWorld() - Constructor for class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
 
HelloWorld - Class in net.sourceforge.seqware.pipeline.plugins
 
HelloWorld() - Constructor for class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
HEMIZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
HETEROZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
HG_19 - Static variable in class com.github.seqware.queryengine.tutorial.Poster
 
HG_19 - Static variable in class com.github.seqware.queryengine.tutorial.PosterSGE
 
hibernateCalls() - Method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
 
hold - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
holdForPeriod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
holdUntilDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
HOMOZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
HTMLTagValidator - Class in net.sourceforge.solexatools.util
 
HTMLTagValidator() - Constructor for class net.sourceforge.solexatools.util.HTMLTagValidator
 
hybridassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 

I

id - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
id - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
 
ID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
IllQualStat - Class in net.sourceforge.seqware.pipeline.modules.qc
Basic QC report This module parses quality report from Illumina pipeline (Gerald) Underlying script: sw_module_parseIllQC.pl Necessary programs: perl Expected output: Ill_QC_summary.csv
IllQualStat() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
 
illumina - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
Illumina2SRF - Class in net.sourceforge.seqware.pipeline.modules.io
This module takes an Illumina Genome Analyzer run folder and converts what it finds there into one SRF per lane.
Illumina2SRF() - Constructor for class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
 
impersonate(SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Set the UUID, very dangerous, this should never be called outside of the backend
impersonate(SGID, SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Set the UUID, very dangerous, this should never be called outside of the backend
ImportConstants - Class in com.github.seqware.queryengine.system.importers.workers
Noticed that a few of the file types repeat a lot of information that we might want to store as fields (and are fields in the old prototype).
ImportConstants() - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
Importer - Class in com.github.seqware.queryengine.system.importers
This looks like a class to control concurrency for multiple ImportWorkers, one per input file
Importer(int) - Constructor for class com.github.seqware.queryengine.system.importers.Importer
 
Importer() - Constructor for class com.github.seqware.queryengine.system.importers.Importer
 
Importer - Class in net.sourceforge.seqware.queryengine.tools.importers
 
Importer(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.Importer
 
Importer() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.Importer
 
ImporterTest - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
 
ImporterTest() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest
 
ImporterTest2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
 
ImporterTest2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest2
 
ImportWorker - Class in com.github.seqware.queryengine.system.importers.workers
Base Worker class, looks like a Bean for storing settings about the file to be converted.
ImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
ImportWorker(String, Importer, String, boolean, int, int, float, boolean, int, boolean, boolean, int) - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
ImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
ImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
ImportWorker(String, Importer, Store, String, boolean, int, int, float, boolean, int, boolean, boolean, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
includeCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
includeIndels - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
includeSNV - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
indirectBIMap - Variable in class com.github.seqware.queryengine.impl.StorageInterface
These tables are created on-the-fly with a referenceID appended in order to separate out Features by Reference
info(Object) - Static method in class com.github.seqware.queryengine.common.Log
See Category.info(Object).
info(Object, Throwable) - Static method in class com.github.seqware.queryengine.common.Log
See Category.info(Object,Throwable).
info(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.info(Object).
info(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.info(Object,Throwable).
informOnError - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
 
informOnStatus - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
 
ini2Map(String, Map<String, String>) - Static method in class com.github.seqware.queryengine.common.MapTools
 
ini2Map(String, Map<String, String>, boolean) - Static method in class com.github.seqware.queryengine.common.MapTools
 
ini2Map(InputStream, Map<String, String>, boolean) - Static method in class com.github.seqware.queryengine.common.MapTools
 
ini2Map(String, Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
 
ini2Map(String, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
 
ini2Map(InputStream, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
 
ini2RichMap(String, Map<String, Map<String, String>>) - Static method in class com.github.seqware.queryengine.common.MapTools
This is a little different than the ini2Map since it allows us to read ini files where key-value annotations on the key-values appear in comments on the previous line above the current such as: key=bam_inputs:type=file:display=T:display_name=BAM Input(s):file_meta_type=application/bam or key=run_ends:type=pulldown:display=T:display_name=Single or Paired Ends:pulldown_items=Single End|1;Paired End|2 The extra information is used by the Portal and Web Service to display interfaces that let people call the workflows correctly.
ini2RichMap(String, Map<String, Map<String, String>>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
This is a little different than the ini2Map since it allows us to read ini files where key-value annotations on the key-values appear in comments on the previous line above the current such as: key=bam_inputs:type=file:display=T:display_name=BAM Input(s):file_meta_type=application/bam or key=run_ends:type=pulldown:display=T:display_name=Single or Paired Ends:pulldown_items=Single End|1;Paired End|2 The extra information is used by the Portal and Web Service to display interfaces that let people call the workflows correctly.
iniString2Map(String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
 
init(FeatureSet, Object...) - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
Initialize this plug-in, this is called once when the plug-in is starting a job
init(FeatureSet, Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
init(FeatureSet, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
 
init(FeatureSet, Object...) - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin
 
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Connect to a database for future use
init(DataSource) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Connect to a database for future use
init(String, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
Connect to a database for future use
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
init() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
 
init() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
init() - Method in class net.sourceforge.seqware.pipeline.module.Module
 
init() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Module initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
The init method is where you put any code needed to setup your module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
The init method is where you put any code needed to setup your module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
The init method is where you put any code needed to setup your module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
The init method is where you put any code needed to setup your module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
The init method is where you put any code needed to setup your module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.Picard
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
All necessary setup for the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix
Initialization of the module.
init() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
init() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
 
init(Request) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
initBinder(HttpServletRequest, ServletRequestDataBinder) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
InMemoryAnalysisSet - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a AnalysisSet.
InMemoryAnalysisSet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet
 
InMemoryAnalysisSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryAnalysisSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet.Builder
 
InMemoryFeaturesAllPlugin - Class in com.github.seqware.queryengine.plugins.inmemory
 
InMemoryFeaturesAllPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesAllPlugin
 
InMemoryFeaturesAllPlugin.FeaturesAllFilter - Class in com.github.seqware.queryengine.plugins.inmemory
 
InMemoryFeaturesAllPlugin.FeaturesAllFilter() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesAllPlugin.FeaturesAllFilter
 
InMemoryFeaturesByAttributesPlugin - Class in com.github.seqware.queryengine.plugins.inmemory
Generic query implementation over all attributes of a Feature (including additional attributes).
InMemoryFeaturesByAttributesPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin
 
InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter - Class in com.github.seqware.queryengine.plugins.inmemory
 
InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter
 
InMemoryFeaturesByFilterPlugin - Class in com.github.seqware.queryengine.plugins.inmemory
Generic query implementation over all attributes of a Feature using a FeatureFilter.
InMemoryFeaturesByFilterPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
 
InMemoryFeaturesByRangePlugin - Class in com.github.seqware.queryengine.plugins.inmemory
Retrieves features based on their chromosomal location.
InMemoryFeaturesByRangePlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByRangePlugin
 
InMemoryFeaturesByRangePlugin.FeaturesByRangeFilter - Class in com.github.seqware.queryengine.plugins.inmemory
 
InMemoryFeaturesByRangePlugin.FeaturesByRangeFilter() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByRangePlugin.FeaturesByRangeFilter
 
InMemoryFeaturesByTagPlugin - Class in com.github.seqware.queryengine.plugins.inmemory
 
InMemoryFeaturesByTagPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByTagPlugin
 
InMemoryFeaturesByTagPlugin.FeaturesByTagFilter - Class in com.github.seqware.queryengine.plugins.inmemory
 
InMemoryFeaturesByTagPlugin.FeaturesByTagFilter() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByTagPlugin.FeaturesByTagFilter
 
InMemoryFeatureSet - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a feature set.
InMemoryFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
InMemoryGroup - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a group.
InMemoryGroup() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
InMemoryGroup.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryGroup.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
 
InMemoryIterable<T> - Class in com.github.seqware.queryengine.util
A bit of a hack class, allows us to have getCount as well as iterable
InMemoryIterable(Collection) - Constructor for class com.github.seqware.queryengine.util.InMemoryIterable
 
InMemoryIterator<T> - Class in com.github.seqware.queryengine.util
An in-memory iterator for unit testing of SeqWareIterator.
InMemoryIterator(Iterator<T>) - Constructor for class com.github.seqware.queryengine.util.InMemoryIterator
Creates a new in-memory SeqWareIterator implementation.
InMemoryQueryFutureImpl<T> - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryQueryFutureImpl() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
 
InMemoryQueryFutureImpl.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryQueryFutureImpl.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl.Builder
 
InMemoryReference - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a reference.
InMemoryReference() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
Anonymous constructor
InMemoryReference.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryReference.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
 
InMemoryReferenceSet - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a reference set.
InMemoryReferenceSet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
 
InMemoryReferenceSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryReferenceSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
 
InMemoryTagSet - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a TagSet.
InMemoryTagSet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
InMemoryTagSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryTagSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
 
input - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
INPUT_FILES_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
inputFile - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
inputs - Variable in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
inputSet - Variable in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
inputSize - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
insert(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
 
insert(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
insert(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
insert(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
 
insert(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
 
insert(File) - Method in interface net.sourceforge.seqware.common.business.FileService
 
insert(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService
 
insert(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
Inserts an instance of ExperimentLibraryDesign into the database.
insert(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
Inserts an instance of Experiment into the database.
insert(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
insert(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
Inserts an instance of ExperimentSpotDesignReadSpec into the database.
insert(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
Inserts an instance of ExperimentSpotDesign into the database.
insert(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
Inserts an instance of File into the database.
insert(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
insert(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
insert(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
insert(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
insert(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
insert(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Inserts an instance of Lane into the database.
insert(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
insert(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
insert(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
insert(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
insert(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
insert(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
insert(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
insert(SequencerRun, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
Inserts an instance of Processing into the database.
insert(Registration, SequencerRun, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
insert(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
insert(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
insert(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
insert(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
Inserts an instance of Project into the database.
insert(RegistrationDTO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
 
insert(String[], InvitationParams, MailSender) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
 
insert(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Inserts an instance of Sample into the database.
insert(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
insert(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Inserts an instance of SequencerRun into the database.
insert(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
This is being used to create a new SequencerRun object and the correct number of assocated Lanes
insert(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
insert(Registration, SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
insert(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
insert(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
insert(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
insert(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
insert(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
insert(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
Inserts an instance of ShareStudy into the database.
insert(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
Inserts an instance of ShareWorkflowRun into the database.
insert(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Inserts an instance of Study into the database.
insert(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
insert(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
Inserts an instance of StudyType into the database.
insert(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
insert(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
insert(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
insert(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
insert(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
insert(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
insert(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
insert(WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
insert(Registration, WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
insert(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
insert(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
insert(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
insert(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
insert(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
insert(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
insert(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
insert(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
insert(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
 
insert(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
 
insert(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
 
insert(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
 
insert(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
 
insert(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
 
insert(SequencerRun, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
insert(Registration, SequencerRun, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
insert(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
insert(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
 
insert(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
insert(RegistrationDTO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
 
insert(String[], InvitationParams, MailSender) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
 
insert(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
insert(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
insert(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
insert(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
insert(SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
insert(Registration, SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
insert(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
insert(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
insert(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
insert(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
insert(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
insert(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
insert(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
insert(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
insert(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
insert(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
 
insert(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
insert(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
insert(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
insert(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
insert(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
Inserts a new WorkflowRun and returns its sw_accession number.
insert(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
insert(WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
insert(Registration, WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
insert(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
insert(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
 
insert(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
insert(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
insert(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
 
insert(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
 
insert(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
 
insert(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
 
insert(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
insert(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
insert(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
 
insert(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
insert(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
insert(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
 
insert(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
 
insert(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
 
insert(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
 
insert(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
Inserts an instance of File into the database.
insert(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
insert(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
insert(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
insert(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
 
insert(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
Inserts an instance of Lane into the database.
insert(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
insert(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO
 
insert(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
 
insert(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
 
insert(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
 
insert(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
Inserts an instance of Lane into the database.
insert(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
insert(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
 
insert(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
 
insert(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
 
insert(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
insert(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
insert(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
 
insert(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
 
insert(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
 
insert(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
insert(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
 
insert(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
 
insert(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
 
insert(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
 
insert(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
Inserts an instance of Registration into the database.
insert(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
 
insert(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
Inserts an instance of Sample into the database.
insert(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
insert(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
 
insert(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
insert(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
insert(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
insert(Registration, SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
insert(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
insert(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
insert(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
insert(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
insert(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
insert(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
Inserts an instance of ShareStudy into the database.
insert(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
Inserts an instance of ShareWorkflowRun into the database.
insert(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
 
insert(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
insert(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
insert(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
 
insert(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
 
insert(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
insert(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
insert(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
insert(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
insert(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
insert(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
insert(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
insert(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
insert(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
insert(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
insert(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
insert(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
 
insert(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
insert(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
insert(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
insert(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
insert(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
 
insert(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
insert(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
 
insert(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
 
insert(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
 
insert(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
 
insert(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
 
insert(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
 
insert(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
 
insert(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
 
insert(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
 
insert(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
 
insert(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
insert(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
insert(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
 
insert(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
insert(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
insert(SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
insert(Registration, SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
insert(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
 
insert(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
 
insert(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
 
insert(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
 
insert(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
 
insert(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
 
insert(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
insert(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
 
insert(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
insert(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
insert(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
 
insert(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
 
insert(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
insert(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
 
insert(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
 
insert(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
Inserts a new WorkflowRun and returns its sw_accession number.
insert(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
insert(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
insert(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
InsertAndReturnNewPrimaryKey(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic
InsertAndReturnNewPrimaryKey(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic
insertFilesAsWorkflowRunParam(WorkflowRun, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
insertFilesAsWorkflowRunParam(Registration, WorkflowRun, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
insertFilesAsWorkflowRunParam(WorkflowRun, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
insertFilesAsWorkflowRunParam(Registration, WorkflowRun, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
INSERTION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
insertLane(Registration, Sample, UploadSequence, FileType) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
insertLane(Registration, Sample, UploadSequence, FileType) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
insertWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
 
InSessionExecutions - Class in net.sourceforge.seqware.common.hibernate
 
InSessionExecutions() - Constructor for class net.sourceforge.seqware.common.hibernate.InSessionExecutions
 
installAnalysisPlugin(AnalysisPluginInterface) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
installAnalysisPlugin(AnalysisPluginInterface) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Install a plug-in so that it can be listed
installBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
installBundle(File, File, boolean, boolean) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
This method allows you to install the workflow bundle to the metadb optionally building a zip file along the way and archiving it to a safe location.
installBundleDirOnly(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
installBundleZipOnly(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
instanceOf(Object, String) - Static method in class net.sourceforge.solexatools.util.TagUtils
 
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
 
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
 
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
 
instrumentModel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
instrumentName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
INT_PARAMETERS - Static variable in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
int_parameters - Variable in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper
parameters that will be handled by the plug-in developer but will not be available to the user
IntegerIdComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
 
IntegerIdComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.IntegerIdComparator
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
internalGetValueMap() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
INVALIDARGUMENT - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
INVALIDFILE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
INVALIDPARAMETERS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
INVALIDPLUGIN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
InvitationParams - Class in net.sourceforge.seqware.common.invitation
 
InvitationParams(String, String, String) - Constructor for class net.sourceforge.seqware.common.invitation.InvitationParams
 
InviteNewUserController - Class in net.sourceforge.solexatools.webapp.controller
 
InviteNewUserController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
 
InviteNewUserSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
InviteNewUserSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController
 
InviteNewUserValidatorController - Class in net.sourceforge.solexatools.webapp.controller
 
InviteNewUserValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
 
Invoice - Class in net.sourceforge.seqware.common.model
 
Invoice() - Constructor for class net.sourceforge.seqware.common.model.Invoice
 
InvoiceDAO - Interface in net.sourceforge.seqware.common.dao
 
InvoiceDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
InvoiceDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
InvoiceDetailsController - Class in net.sourceforge.solexatools.webapp.controller
 
InvoiceDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
 
InvoiceService - Interface in net.sourceforge.seqware.common.business
 
invoiceService - Variable in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
 
invoiceService - Variable in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
 
InvoiceServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
InvoiceServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
isActiveTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
isActiveTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
isAuthenticated(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security
 
isCheckEmail(String) - Static method in class net.sourceforge.solexatools.validation.LoginValidator
 
isComplete() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
Non-blocking call to determine whether the result is ready
isComplete() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
isComplete() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
isCompressed() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
isCompressed() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
isConfigError(Throwable) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos
 
isCreateConsequenceAnnotationDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
isCreateCoverageDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
isCreateDbSNPAnnotationDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
isCreateMismatchDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
isDebug() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
 
isDescendantOf(String) - Method in class com.github.seqware.queryengine.model.Tag
Tests whether the given tag is a parent of this tag -- making this tag a descendant of the parameter tag.
isDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
isDone() - Method in class com.github.seqware.queryengine.model.Analysis
 
isDone() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
 
isDone() - Method in interface com.github.seqware.queryengine.model.QueryFuture
Returns true iff the query is ready with its results.
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
isDuplicateFile(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
isEnd() - Method in class net.sourceforge.solexatools.util.PageInfo
 
isExists(String, String) - Method in interface net.sourceforge.seqware.common.business.FileService
 
isExists(String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
isExistsShare(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
 
isExistsShare(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
 
isExistsShare(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
isExistsShare(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
isExpires() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
isExpires() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return true iff this expires
isFinalized() - Method in class net.sourceforge.seqware.common.model.Invoice
 
isFullyPaid() - Method in class net.sourceforge.seqware.common.model.Invoice
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
isIncludeCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
isIncludeCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
isIncludeIndels() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
isIncludeIndels() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
isIncludeIndels() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
isIncludeSNV() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
isIncludeSNV() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
isIncludeSNVs() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
isInstalled() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
isJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
 
isJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
 
isLaunch() - Method in class net.sourceforge.seqware.common.model.Workflow
 
isLIMSAdmin() - Method in class net.sourceforge.seqware.common.model.Registration
 
isLocked() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated.  
isMetadataOverridden() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
isPayee() - Method in class net.sourceforge.seqware.common.model.Registration
 
isPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow
 
isProvisionFilesJob() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
isProvisionFilesJob() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusSeqwareModuleJob
 
isPublic() - Method in class net.sourceforge.seqware.common.model.Workflow
 
isReadOnly() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
isRequireFiles() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
isReturnIds() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
isSortable() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
isStart() - Method in class net.sourceforge.solexatools.util.PageInfo
 
isTaskGroup() - Method in class net.sourceforge.seqware.common.model.Processing
 
isTechnician() - Method in class net.sourceforge.seqware.common.model.Registration
 
isTombstone() - Method in class com.github.seqware.queryengine.util.FSGID
Back-end method for Features stored within high capacity featuresets
isUsePairedFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
isVerbose() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
itemRgb - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
iterator() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterable
 
iterator() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
 
iterator() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
iterator() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
iterator() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
iterator() - Method in class com.github.seqware.queryengine.util.InMemoryIterable
 
iterator() - Method in class com.github.seqware.queryengine.util.SGIDIterable
 
IUS - Class in net.sourceforge.seqware.common.model
 
IUS() - Constructor for class net.sourceforge.seqware.common.model.IUS
 
IUS_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
IUS_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
 
IUS_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
IUS_TAG - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
IUS_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
IUSAttribute - Class in net.sourceforge.seqware.common.model
IusAttribute generated by hbm2java
IUSAttribute() - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute
 
IUSAttribute(int, IUS) - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute
 
IUSAttribute(int, IUS, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute
 
IUSAttributeDAO - Interface in net.sourceforge.seqware.common.dao
 
IUSAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
IUSAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
 
IUSController - Class in net.sourceforge.solexatools.webapp.controller
 
IUSController() - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSController
 
IUSController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSController
 
IUSDAO - Interface in net.sourceforge.seqware.common.dao
 
IUSDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
IUSDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
IusDto - Class in net.sourceforge.seqware.webservice.dto
 
IusDto() - Constructor for class net.sourceforge.seqware.webservice.dto.IusDto
 
IusFilesResource - Interface in net.sourceforge.seqware.webservice.resources.tables
 
IusFilesServerResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
IusFilesServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource
 
IusIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
IusIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
 
IUSLink - Class in net.sourceforge.seqware.common.model
IusLink generated by hbm2java
IUSLink() - Constructor for class net.sourceforge.seqware.common.model.IUSLink
 
IUSLink(int, IUS, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSLink
 
IUSLink(int, IUS, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSLink
 
IUSLinkDAO - Interface in net.sourceforge.seqware.common.dao.hibernate
 
IUSLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
IUSLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
 
IUSList - Class in net.sourceforge.seqware.common.model.lists
 
IUSList() - Constructor for class net.sourceforge.seqware.common.model.lists.IUSList
 
IusResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
IusResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusResource
 
IusSearchResource - Interface in net.sourceforge.seqware.webservice.resources.tables
 
IusSearchServerResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
IusSearchServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource
 
IUSService - Interface in net.sourceforge.seqware.common.business
 
IUSServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
IUSServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
IUSSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
IUSSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSSetupController
 

J

JavaJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
JavaJob(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JavaJob
 
JaxbObject<T> - Class in net.sourceforge.seqware.common.util.xmltools
Convenience class for converting objects into JAXB XML.
JaxbObject() - Constructor for class net.sourceforge.seqware.common.util.xmltools.JaxbObject
JAXB has a memory leak when it comes to making new JAXBContext instances, so one JAXBContext is created for the entire lifetime of the program and initialized with all of the classes that we marshal and unmarshal at the moment, as per the instructions at * http://whileonefork.blogspot.com/2010/09/leaking-of-jaxb.html and * http://jaxb.java.net/guide/Performance_and_thread_safety.html .
jdbcTemplate() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig
 
JndiDatasourceCreator - Class in net.sourceforge.seqware.common.util.testtools
 
JndiDatasourceCreator() - Constructor for class net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator
 
job - Variable in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
Job - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
Job() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
Job(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
JobModule - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
JobModule(Module) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
 
jobObj - Variable in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
JobProfile - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
JobProfile(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
 
JSON - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
JSON - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
JsonUtil - Class in net.sourceforge.seqware.common.util.jsontools
 
JsonUtil() - Constructor for class net.sourceforge.seqware.common.util.jsontools.JsonUtil
 

K

KEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
keyIndex - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
keys() - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
 
KEYVALUE_OUT_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
 
keyvalues - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
KryoSerialization - Class in com.github.seqware.queryengine.impl
 
KryoSerialization() - Constructor for class com.github.seqware.queryengine.impl.KryoSerialization
 

L

label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
 
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
 
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
 
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
 
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
 
labName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
Lane - Class in net.sourceforge.seqware.common.model
 
Lane() - Constructor for class net.sourceforge.seqware.common.model.Lane
 
LANE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
LANE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
LANE_NUM - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
LANE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
 
LANE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
LANE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
LaneAttribute - Class in net.sourceforge.seqware.common.model
LaneAttribute generated by hbm2java
LaneAttribute() - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute
 
LaneAttribute(int, Lane) - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute
 
LaneAttribute(int, Lane, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute
 
LaneAttributeDAO - Interface in net.sourceforge.seqware.common.dao.hibernate
 
LaneAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
LaneAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
 
LaneController - Class in net.sourceforge.solexatools.webapp.controller
LaneController
LaneController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneController
 
LaneController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneController
 
LaneDAO - Interface in net.sourceforge.seqware.common.dao
 
LaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
LaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
LaneIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
LaneIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
 
LaneLink - Class in net.sourceforge.seqware.common.model
LaneLink generated by hbm2java
LaneLink() - Constructor for class net.sourceforge.seqware.common.model.LaneLink
 
LaneLink(int, Lane, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneLink
 
LaneLink(int, Lane, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneLink
 
LaneLinkDAO - Interface in net.sourceforge.seqware.common.dao.hibernate
 
LaneLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
LaneLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
 
LaneList - Class in net.sourceforge.seqware.common.model.lists
 
LaneList() - Constructor for class net.sourceforge.seqware.common.model.lists.LaneList
 
LaneResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
LaneResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LaneResource
 
LaneSampleAssociateController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
LaneSampleAssociateController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
LaneSampleAssociateSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
LaneSampleAssociateSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
 
LaneService - Interface in net.sourceforge.seqware.common.business
 
LaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
LaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
LaneSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
LaneSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSetupController
 
LaneValidator - Class in net.sourceforge.solexatools.validation
 
LaneValidator() - Constructor for class net.sourceforge.solexatools.validation.LaneValidator
 
LASTNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
launchBundle(String, String, String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
FIXME: need to add metadata writeback
launchBundle(String, String, String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
 
launchInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
This method just needs a sw_accession value from the workflow table and an ini file(s) in order to launch a workflow.
launchInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
 
launchScheduledBundle(String, String, boolean, boolean) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
This method just needs a sw_accession value from the workflow_run table to launch a workflow.
launchScheduledBundle(String, String, boolean, boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
 
LaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller
 
LaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
 
LaunchWorkflowListController - Class in net.sourceforge.solexatools.webapp.controller
 
LaunchWorkflowListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
 
LaunchWorkflowListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
 
LaunchWorkflowListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
LaunchWorkflowSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
LaunchWorkflowSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
 
LaunchWorkflowUtil - Class in net.sourceforge.solexatools.util
 
LaunchWorkflowUtil() - Constructor for class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
LazyFeaturesByAttributesPlugin - Class in com.github.seqware.queryengine.plugins.lazyinmemory
Generic query implementation over all attributes of a Feature (including additional attributes).
LazyFeaturesByAttributesPlugin() - Constructor for class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin
 
LazyFeatureSet - Class in com.github.seqware.queryengine.model.impl.lazy
An "lazy" representation of a feature set.
LazyFeatureSet() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Creates an in-memory feature set.
LazyFeatureSet.BatchedRowFeatureListsIterator - Class in com.github.seqware.queryengine.model.impl.lazy
Go through the raw iterator from the underlying storage type and batch up the FeatureLists and return them by rows
LazyFeatureSet.BatchedRowFeatureListsIterator() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
 
LazyFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.lazy
 
LazyFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
LazyFeatureSet.ConsolidatedFeatureIterator - Class in com.github.seqware.queryengine.model.impl.lazy
Iterates through Features given FeatureLists sorted by rows
LazyFeatureSet.ConsolidatedFeatureIterator() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
 
LazyLatestReference<T extends Atom> - Class in com.github.seqware.queryengine.util
Lazy reference class, needed if we wish to reduce the number of random accesses when deserializing objects or creating HBase specific model implementations.
LazyLatestReference(Class<T>) - Constructor for class com.github.seqware.queryengine.util.LazyLatestReference
 
LazyMolSet<S extends MolSetInterface,T> - Interface in com.github.seqware.queryengine.model.impl
 
LazyReference<T extends Atom> - Class in com.github.seqware.queryengine.util
Lazy reference class, needed if we wish to reduce the number of random accesses when de-serializing objects or creating HBase specific model implementations.
LazyReference(Class<T>) - Constructor for class com.github.seqware.queryengine.util.LazyReference
 
LEASTSIGBITS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
LibrariesResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
LibrariesResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource
 
libraryconstructionprotocol - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibraryDAO - Interface in net.sourceforge.seqware.common.dao
 
LibraryDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
LibraryDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
 
librarydescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
LibraryDto - Class in net.sourceforge.seqware.webservice.dto
 
LibraryDto() - Constructor for class net.sourceforge.seqware.webservice.dto.LibraryDto
 
LibraryIdentityDto - Class in net.sourceforge.seqware.webservice.dto
 
LibraryIdentityDto() - Constructor for class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
 
librarylayout - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
libraryname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibraryResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
LibraryResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibraryResource
 
LibrarySelection - Class in net.sourceforge.seqware.common.model
 
LibrarySelection() - Constructor for class net.sourceforge.seqware.common.model.LibrarySelection
 
libraryselection - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibrarySelectionDAO - Interface in net.sourceforge.seqware.common.dao
 
LibrarySelectionDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
LibrarySelectionDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
 
LibrarySelectionService - Interface in net.sourceforge.seqware.common.business
 
LibrarySelectionServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
LibrarySelectionServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
 
LibraryService - Interface in net.sourceforge.seqware.common.business
 
LibraryServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
LibraryServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
 
LibrarySource - Class in net.sourceforge.seqware.common.model
 
LibrarySource() - Constructor for class net.sourceforge.seqware.common.model.LibrarySource
 
librarysource - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibrarySourceDAO - Interface in net.sourceforge.seqware.common.dao
 
LibrarySourceDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
LibrarySourceDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
 
LibrarySourceService - Interface in net.sourceforge.seqware.common.business
 
LibrarySourceServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
LibrarySourceServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
 
LibraryStrategy - Class in net.sourceforge.seqware.common.model
 
LibraryStrategy() - Constructor for class net.sourceforge.seqware.common.model.LibraryStrategy
 
librarystrategy - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibraryStrategyDAO - Interface in net.sourceforge.seqware.common.dao
 
LibraryStrategyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
LibraryStrategyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
 
LibraryStrategyService - Interface in net.sourceforge.seqware.common.business
 
LibraryStrategyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
LibraryStrategyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
 
linkAccessionAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
linkAccessionAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
linkProcessingAndFile(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
TODO: needs to support more relationship types, but will need to add to the SQL schema to support this
linkWorkflowRunAndParent(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
TODO: needs to support more relationship types, but will need to add to the SQL schema to support this
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
linkWorkflowRunAndParent(WorkflowRun, int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
 
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
 
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
list(Study) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
 
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
 
list() - Method in interface net.sourceforge.seqware.common.business.FileService
 
list() - Method in interface net.sourceforge.seqware.common.business.FileTypeService
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
list(Study) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
list(Registration, String) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
list(List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
list() - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
list(Registration, String) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
list() - Method in interface net.sourceforge.seqware.common.business.IUSService
 
list(List<Integer>) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
list() - Method in interface net.sourceforge.seqware.common.business.LaneService
 
list() - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
 
list() - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
 
list() - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
 
list() - Method in interface net.sourceforge.seqware.common.business.OrganismService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.OrganismService
 
list() - Method in interface net.sourceforge.seqware.common.business.PlatformService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.PlatformService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
 
list() - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
list() - Method in interface net.sourceforge.seqware.common.business.SampleSearchService
 
list() - Method in interface net.sourceforge.seqware.common.business.SampleService
 
list() - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
list() - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
list() - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
list() - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
list() - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
list() - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
list() - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
list() - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
list() - Method in interface net.sourceforge.seqware.common.business.StudyService
 
list() - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
 
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
list(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
list(Study) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
list(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
list(Registration, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
list(List<Integer>) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
 
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
 
list(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
 
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
list() - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
list(Registration, String) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
list(List<Integer>) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO
 
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
 
list(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
 
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
ListBEDExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters
 
ListBEDExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.ListBEDExporter
 
listComplete() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
listComplete() - Method in interface net.sourceforge.seqware.common.business.SampleService
 
listComplete() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
listComplete() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
listFile(Registration, String, List<File>, String[], String[]) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
listFile(Registration, String, List<File>, String[], String[]) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
listFilesRecursive(File, ArrayList<File>) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
listIncomplete() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
listIncomplete() - Method in interface net.sourceforge.seqware.common.business.SampleService
 
listIncomplete() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
listIncomplete() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
listInstalledWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
listInstalledWorkflows() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
listRelatedWorkflows(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listRelatedWorkflows(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listRelatedWorkflows(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
listRelatedWorkflows(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
listRunning(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listRunning(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listRunning(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listRunning(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listRunning(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
listRunning(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
listSample(Registration) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
listSample(Registration) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
listSample(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
listSample(Registration) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
listSequencerRunsWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
listSequencerRunsWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
listSharedWithMeWithSample(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listSharedWithMeWithSample(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listStudyHasFile(Registration, String, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
listStudyHasFile(Registration, String, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
listStudyHasFile(Registration, String, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
listStudyHasFile(Registration, String, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
listWithHasFile(SortedSet<Experiment>, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
listWithHasFile(SortedSet<Experiment>, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
listWithHasFile(SortedSet<IUS>, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
listWithHasFile(SortedSet<Lane>, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
listWithHasFile(Integer, SortedSet<Sample>, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
listWithHasFile(List<Study>) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
listWithHasFile(List<Study>, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
listWithHasFile(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
listWithHasFile(SortedSet<IUS>, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
listWithHasFile(SortedSet<Lane>, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
listWithHasFile(Integer, SortedSet<Sample>, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
listWithHasFile(List<Study>) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
listWithHasFile(List<Study>, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
listWithHasFile(List<WorkflowRun>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
listWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
listWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
LiveTagResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
LiveTagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.LiveTagResource
 
LoadIndexPageController - Class in net.sourceforge.solexatools.webapp.controller
 
LoadIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
 
LocatableModel - Class in net.sourceforge.seqware.queryengine.backend.model
 
LocatableModel() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
LocatableSecondaryCursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
 
LocatableSecondaryCursorIterator(SecondaryCursor, DatabaseEntry, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator
 
LocatableSecondaryCursorIterator(SecondaryCursor, DatabaseEntry, ContigPosition, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator
 
locateFile(String) - Method in class net.sourceforge.seqware.common.metadata.Metadata
 
lockAndAppend(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools
Try to acquire lock.
lockAndAppendLine(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools
 
LockingFileTools - Class in net.sourceforge.seqware.common.util.filetools.lock
 
LockingFileTools() - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools
 
Log - Class in com.github.seqware.queryengine.common
 
Log - Class in net.sourceforge.seqware.common.util
 
LOG - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
 
log(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
 
log(String) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC
 
log(String) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase
 
LogAspect - Class in net.sourceforge.seqware.pipeline.runner
This is a test class Created by IntelliJ IDEA.
LogAspect() - Constructor for class net.sourceforge.seqware.pipeline.runner.LogAspect
 
logging() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig
 
LoginController - Class in net.sourceforge.solexatools.webapp.controller
LoginController
LoginController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LoginController
 
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.Authentication
 
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
 
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos
Get boolean true/false based on onyen/password pair.
LoginValidator - Class in net.sourceforge.solexatools.validation
 
LoginValidator() - Constructor for class net.sourceforge.solexatools.validation.LoginValidator
 
LogoutController - Class in net.sourceforge.solexatools.webapp.controller
 
LogoutController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LogoutController
 
ls454 - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 

M

m2pb(Analysis) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisIO
 
m2pb(AnalysisSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisSetIO
 
m2pb(Feature) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
 
m2pb(FeatureList) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
 
m2pb(FeatureSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
 
m2pb(FSGID) - Static method in class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO
 
m2pb(Group) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO
 
m2pb(T) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface
Convert from model to protein buffer object
m2pb(Reference) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
 
m2pb(ReferenceSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
 
m2pb(SGID) - Static method in class com.github.seqware.queryengine.impl.protobufIO.SGIDIO
 
m2pb(Tag) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO
 
m2pb(TagSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
 
m2pb(Tag) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
 
m2pb(User) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO
 
main(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Command-line interface
main(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper
 
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter
 
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.OBOImporter
 
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Command-line interface
main(String[]) - Static method in class com.github.seqware.queryengine.system.ReferenceCreator
 
main(String[]) - Static method in class com.github.seqware.queryengine.system.TagSetCreator
 
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.BrianTest
 
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.GITest
 
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.Poster
 
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.PosterSGE
 
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
main(String[]) - Static method in class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup
 
main(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.module.TestModule
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.modules.examples.MultiEchoTest
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.PluginRunner
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner2
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.ReportTest
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.UnZip
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.Zip
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC
A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase
A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCOld
A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.BlobReaderWriter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseRead2
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest2
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest
Main entry point.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2
Main entry point.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.annotators.AnnotateVariantsWithContigAndZygosity
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.BEDExporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.ListBEDExporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.TagDumper
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.TextDumper
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.WIGExporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.FeatureImporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.PileupCoverageImporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationByPositionImporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationImporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceByPositionImporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceImporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantImporter
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.iterators.CoverageIteratorProcessor
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.iterators.VariantIteratorProcessor
 
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantAndCoverageDatabases
A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantDatabases
FIXME: add param to pass in range to compare over eg chr22 or chr1:123-1231231
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain
 
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.importers.OBOImporter
Import a set of Tag specifications into a new TagSet.
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.ReferenceCreator
Create a reference given just a name for the new reference to be created.
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.TagSetCreator
Create a reference given just a name for the new reference to be created.
MakeBigWig - Class in net.sourceforge.seqware.pipeline.modules.alignment
Generate bigWig file from a BAM file.
MakeBigWig() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
 
makeReport(String) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport
 
manageFlushedObjects(List<Map.Entry<String, SimpleModelManager.AtomStatePair>>) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
ManageWorkflowsController - Class in net.sourceforge.solexatools.webapp.controller
 
ManageWorkflowsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
 
map(Feature, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
map(Feature, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
 
map(Feature, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin
 
map(T, S) - Method in interface com.github.seqware.queryengine.plugins.MapReducePlugin
Mapping implementation that singles out desired atoms into a mapped set.
mapExpandVariables(Map) - Static method in class com.github.seqware.queryengine.common.MapTools
 
mapExpandVariables(Map) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
 
mapInit() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
mapInit() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
 
mapInit() - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin
 
mapInit() - Method in interface com.github.seqware.queryengine.plugins.MapReducePlugin
 
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
This maps processing_id to sw_accession for that event.
mapProcessingIdToAccession(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
This maps processing_id to sw_accession for that event.
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
MapReducePlugin<T extends Atom,S extends MolSetInterface> - Interface in com.github.seqware.queryengine.plugins
An abstracted map-reduce interface.
MapReduceTest - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
TODO: > iterate over each row and pull out variant objects > check to see if both variants exists at position > if they do then increment counter > write the counter to an hdfs file > need to figure out how to pass parameters to map and reduce classes!
MapReduceTest() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest
 
MapReduceTest2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
TODO: > iterate over each row and pull out variant objects > check to see if both variants exists at position > if they do then increment counter > write the counter to an hdfs file > need to figure out how to pass parameters to map and reduce classes!
MapReduceTest2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2
 
MapSplice - Class in net.sourceforge.seqware.pipeline.modules.alignment
Align reads with via MapSplice This module launches a MapSplice alignment of given reads file(s) against given reference sequences files.
MapSplice() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
 
mapString2Int(Map) - Static method in class com.github.seqware.queryengine.common.MapTools
 
mapString2Int(Map) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
 
MapTools - Class in com.github.seqware.queryengine.common
 
MapTools() - Constructor for class com.github.seqware.queryengine.common.MapTools
 
MapTools - Class in net.sourceforge.seqware.common.util.maptools
 
MapTools() - Constructor for class net.sourceforge.seqware.common.util.maptools.MapTools
 
markDatabaseChanged() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
 
markDatabaseChanged() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
 
marshal(Set<File>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
 
marshal(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
 
marshal(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
 
marshal(String) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeXML
 
marshal(T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject
Turn an object into XML using JAXB and provide the result in a StreamResult.
marshalToDocument(T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject
Turn an object into XML using JAXB and provide the result in a StreamResult.
marshalToDocument(JaxbObject, Object) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
 
MAX_BASE - Static variable in class com.github.seqware.queryengine.kernel.Compression
 
maxCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
maximumMappingQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
maxThreads - Variable in class com.github.seqware.queryengine.system.importers.Importer
 
maxThreads - Variable in class net.sourceforge.seqware.queryengine.tools.importers.Importer
 
maxThreads - Static variable in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
 
MAXVERSIONS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
MD5Generator - Class in net.sourceforge.seqware.common.util
Utility class for calculating MD5 hash on a file's contents.
MD5Generator() - Constructor for class net.sourceforge.seqware.common.util.MD5Generator
 
md5sum(String) - Method in class net.sourceforge.seqware.common.util.MD5Generator
Returns a 32 character representation of the MD5 hash of the specified file's content.
md5sumFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
member - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF
 
member - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS
 
members - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
merge(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
merge(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
merge(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
merge(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
merge(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
merge(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
merge(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
merge(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
merge(String, String, Map) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker
 
mergeAcl(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
mergeAtom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeFeatureSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergeFrom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergeFrom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeFrom(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
mergeFrom(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeFrom(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeFrom(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
mergeFrom(QueryEngine.AnalysisPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
mergeFrom(QueryEngine.AnalysisSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
mergeFrom(QueryEngine.FeatureListPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergeFrom(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeFrom(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeFrom(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
mergeFrom(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeFrom(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeFrom(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeFrom(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeFrom(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeGrp(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergePrecedingID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergePrecedingID(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergePrecedingVersion(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergePrecedingVersion(QueryEngine.AnalysisPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
mergePrecedingVersion(QueryEngine.AnalysisSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
mergePrecedingVersion(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergePrecedingVersion(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergePrecedingVersion(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergePrecedingVersion(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergePrecedingVersion(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergePrecedingVersion(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergePrecedingVersion(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeReferenceID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergeSgid(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergeSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeTagSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeUser(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeVSGIDRef(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
Metadata - Class in net.sourceforge.seqware.common.metadata
 
Metadata() - Constructor for class net.sourceforge.seqware.common.metadata.Metadata
 
metadata - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
metadata - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
metadata - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
Metadata - Class in net.sourceforge.seqware.pipeline.plugins
This plugin currently lets users creation a limited set of table rows in the database from the command line.
Metadata() - Constructor for class net.sourceforge.seqware.pipeline.plugins.Metadata
 
metadata - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
MetadataDB - Class in net.sourceforge.seqware.common.metadata
 
MetadataDB() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataDB
 
MetadataDB - Class in net.sourceforge.seqware.queryengine.webservice.model
 
MetadataDB() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
MetadataInterface - Interface in net.sourceforge.seqware.common.metadata
 
METADATAINVALIDIDCHAIN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
MetadataNoConnection - Class in net.sourceforge.seqware.common.metadata
 
MetadataNoConnection() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
MetadataWS - Class in net.sourceforge.seqware.common.metadata
TODO: this needs to setup rows in experiment_library_design and experiment_spot_design
MetadataWS() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataWS
 
MetadataWS.LowLevel - Class in net.sourceforge.seqware.common.metadata
 
MetadataWS.LowLevel(String, String, String) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
metaMap - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
minCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
minSnpQuality - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
MINUS_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchAAChangeBlosumScore - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchAminoAcidChange - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchChr - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchCodonChange - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchCodonPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
MismatchConsequenceReportProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
 
MismatchConsequenceReportProcessor(String, Store, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor
 
MismatchConsequenceReportProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor
 
MismatchesResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
MismatchesResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.MismatchesResource
 
mismatchId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
MismatchResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
MismatchResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.MismatchResource
 
mismatchStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchStop - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
Model - Class in net.sourceforge.seqware.queryengine.backend.model
 
Model() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Model
 
ModelInterface - Interface in net.sourceforge.seqware.queryengine.backend.model
 
ModelUtil - Class in net.sourceforge.solexatools.util
 
ModelUtil() - Constructor for class net.sourceforge.solexatools.util.ModelUtil
 
modify - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
modifyIniFile(String, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
Module - Class in net.sourceforge.seqware.pipeline.module
 
Module() - Constructor for class net.sourceforge.seqware.pipeline.module.Module
 
MODULE - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
 
Module - Enum in net.sourceforge.seqware.pipeline.workflowV2.model
 
ModuleInterface - Interface in net.sourceforge.seqware.pipeline.module
This interface defines the required behavior of a SeqWare module.
ModuleMethod - Enum in net.sourceforge.seqware.pipeline.module
Enumeration class for ModuleMethod Created by IntelliJ IDEA.
ModuleRunner - Class in net.sourceforge.seqware.pipeline.plugins
 
ModuleRunner() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
Molecule<T extends Molecule> - Interface in com.github.seqware.queryengine.model
Defines core functionality that is shared by classes that are controlled by permissions and are atoms
MoleculeImpl<T extends Molecule> - Class in com.github.seqware.queryengine.model.impl
Implements core functionality that is shared by classes that are controlled by permissions and Versionable, Taggable, TTLable via AtomImpl)
MoleculeImpl() - Constructor for class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
MolSetInterface<S extends MolSetInterface,T> - Interface in com.github.seqware.queryengine.model.interfaces
Abstracts out some of the semantics for interacting with each of our Set classes.
MOSTSIGBITS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
MRFeaturesAllPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr
Implements the "get all features in a feature set" query
MRFeaturesAllPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesAllPlugin
 
MRFeaturesByAttributesPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr
Implements the tag queries
MRFeaturesByAttributesPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByAttributesPlugin
 
MRFeaturesByFilterPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr
Implements the generic queries which independently decide on whether a Feature is included in a result.
MRFeaturesByFilterPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByFilterPlugin
 
MRFeaturesByRangePlugin - Class in com.github.seqware.queryengine.plugins.hbasemr
Implements queries by range operations
MRFeaturesByRangePlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByRangePlugin
 
MRFeaturesByTagsPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr
Implements queries by range operations
MRFeaturesByTagsPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByTagsPlugin
 
MRFeatureSetCountPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr
Counts the number of Features in a FeatureSet
MRFeatureSetCountPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin
 
MRHBaseModelManager - Class in com.github.seqware.queryengine.impl
A Simple implementation of the CreateUpdateManager interface.
MRHBaseModelManager() - Constructor for class com.github.seqware.queryengine.impl.MRHBaseModelManager
 
MRHBasePersistentBackEnd - Class in com.github.seqware.queryengine.impl
Implement HBase optimizations for the back-end.
MRHBasePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
 
MRLazyFeatureSet - Class in com.github.seqware.queryengine.model.impl.hbasemrlazy
An "lazy" representation of a feature set.
MRLazyFeatureSet() - Constructor for class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet
Creates an lazy M/R using feature set.
MRLazyFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.hbasemrlazy
 
MRLazyFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet.Builder
 
MRVCFDumperPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr
This plug-in implements a quick and dirty export using Map/Reduce TODO: Copy from HDFS and parse key value file to VCF properly.
MRVCFDumperPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin
 
MultiEchoTest - Class in net.sourceforge.seqware.pipeline.modules.examples
 
MultiEchoTest() - Constructor for class net.sourceforge.seqware.pipeline.modules.examples.MultiEchoTest
 
multiplier - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
mutatedGenomicSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mutatedTranslatedSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 

N

naiveRun(String[]) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter
Import a set of Features into a particular specified reference.
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileTypeService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileUploadService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.InvoiceService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.IUSService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.LaneService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibrarySelectionService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibrarySourceService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibraryStrategyService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.OrganismService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.PlatformService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.ProcessingService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.ProjectService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.RegistrationService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.SampleService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.SequencerRunService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.ShareStudyService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.StudyService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.StudyTypeService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowService
 
name - Variable in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
name - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
name - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
name - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
NAMESPACE - Variable in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusAbstract
 
NEGATIVE_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
net.sourceforge.seqware.common - package net.sourceforge.seqware.common
 
net.sourceforge.seqware.common.business - package net.sourceforge.seqware.common.business
 
net.sourceforge.seqware.common.business.impl - package net.sourceforge.seqware.common.business.impl
 
net.sourceforge.seqware.common.dao - package net.sourceforge.seqware.common.dao
 
net.sourceforge.seqware.common.dao.hibernate - package net.sourceforge.seqware.common.dao.hibernate
 
net.sourceforge.seqware.common.err - package net.sourceforge.seqware.common.err
 
net.sourceforge.seqware.common.factory - package net.sourceforge.seqware.common.factory
 
net.sourceforge.seqware.common.hibernate - package net.sourceforge.seqware.common.hibernate
 
net.sourceforge.seqware.common.hibernate.reports - package net.sourceforge.seqware.common.hibernate.reports
 
net.sourceforge.seqware.common.invitation - package net.sourceforge.seqware.common.invitation
 
net.sourceforge.seqware.common.metadata - package net.sourceforge.seqware.common.metadata
 
net.sourceforge.seqware.common.metadata.ProcessingTaskGroup - package net.sourceforge.seqware.common.metadata.ProcessingTaskGroup
 
net.sourceforge.seqware.common.model - package net.sourceforge.seqware.common.model
 
net.sourceforge.seqware.common.model.adapters - package net.sourceforge.seqware.common.model.adapters
 
net.sourceforge.seqware.common.model.comparator - package net.sourceforge.seqware.common.model.comparator
 
net.sourceforge.seqware.common.model.lists - package net.sourceforge.seqware.common.model.lists
 
net.sourceforge.seqware.common.module - package net.sourceforge.seqware.common.module
 
net.sourceforge.seqware.common.security - package net.sourceforge.seqware.common.security
 
net.sourceforge.seqware.common.util - package net.sourceforge.seqware.common.util
 
net.sourceforge.seqware.common.util.configtools - package net.sourceforge.seqware.common.util.configtools
 
net.sourceforge.seqware.common.util.exceptiontools - package net.sourceforge.seqware.common.util.exceptiontools
 
net.sourceforge.seqware.common.util.filetools - package net.sourceforge.seqware.common.util.filetools
 
net.sourceforge.seqware.common.util.filetools.lock - package net.sourceforge.seqware.common.util.filetools.lock
 
net.sourceforge.seqware.common.util.filetools.validate - package net.sourceforge.seqware.common.util.filetools.validate
 
net.sourceforge.seqware.common.util.freemarker - package net.sourceforge.seqware.common.util.freemarker
 
net.sourceforge.seqware.common.util.iotools - package net.sourceforge.seqware.common.util.iotools
 
net.sourceforge.seqware.common.util.jsontools - package net.sourceforge.seqware.common.util.jsontools
 
net.sourceforge.seqware.common.util.maptools - package net.sourceforge.seqware.common.util.maptools
 
net.sourceforge.seqware.common.util.processtools - package net.sourceforge.seqware.common.util.processtools
 
net.sourceforge.seqware.common.util.processtools.stderr - package net.sourceforge.seqware.common.util.processtools.stderr
 
net.sourceforge.seqware.common.util.processtools.stdout - package net.sourceforge.seqware.common.util.processtools.stdout
 
net.sourceforge.seqware.common.util.runtools - package net.sourceforge.seqware.common.util.runtools
 
net.sourceforge.seqware.common.util.testtools - package net.sourceforge.seqware.common.util.testtools
 
net.sourceforge.seqware.common.util.workflowtools - package net.sourceforge.seqware.common.util.workflowtools
 
net.sourceforge.seqware.common.util.xmltools - package net.sourceforge.seqware.common.util.xmltools
 
net.sourceforge.seqware.metadb.util - package net.sourceforge.seqware.metadb.util
 
net.sourceforge.seqware.pipeline.bundle - package net.sourceforge.seqware.pipeline.bundle
 
net.sourceforge.seqware.pipeline.daxgenerator - package net.sourceforge.seqware.pipeline.daxgenerator
 
net.sourceforge.seqware.pipeline.decider - package net.sourceforge.seqware.pipeline.decider
 
net.sourceforge.seqware.pipeline.deciders - package net.sourceforge.seqware.pipeline.deciders
 
net.sourceforge.seqware.pipeline.module - package net.sourceforge.seqware.pipeline.module
This package provides the SeqWare module interface and API, including common code and classes.
net.sourceforge.seqware.pipeline.module.ann - package net.sourceforge.seqware.pipeline.module.ann
 
net.sourceforge.seqware.pipeline.modules - package net.sourceforge.seqware.pipeline.modules
 
net.sourceforge.seqware.pipeline.modules.alignment - package net.sourceforge.seqware.pipeline.modules.alignment
 
net.sourceforge.seqware.pipeline.modules.alignment.bwa - package net.sourceforge.seqware.pipeline.modules.alignment.bwa
 
net.sourceforge.seqware.pipeline.modules.BamFilters - package net.sourceforge.seqware.pipeline.modules.BamFilters
 
net.sourceforge.seqware.pipeline.modules.examples - package net.sourceforge.seqware.pipeline.modules.examples
 
net.sourceforge.seqware.pipeline.modules.io - package net.sourceforge.seqware.pipeline.modules.io
 
net.sourceforge.seqware.pipeline.modules.qc - package net.sourceforge.seqware.pipeline.modules.qc
 
net.sourceforge.seqware.pipeline.modules.quantification - package net.sourceforge.seqware.pipeline.modules.quantification
 
net.sourceforge.seqware.pipeline.modules.queryengine - package net.sourceforge.seqware.pipeline.modules.queryengine
 
net.sourceforge.seqware.pipeline.modules.utilities - package net.sourceforge.seqware.pipeline.modules.utilities
 
net.sourceforge.seqware.pipeline.plugin - package net.sourceforge.seqware.pipeline.plugin
 
net.sourceforge.seqware.pipeline.plugins - package net.sourceforge.seqware.pipeline.plugins
 
net.sourceforge.seqware.pipeline.runner - package net.sourceforge.seqware.pipeline.runner
 
net.sourceforge.seqware.pipeline.tools - package net.sourceforge.seqware.pipeline.tools
 
net.sourceforge.seqware.pipeline.workflow - package net.sourceforge.seqware.pipeline.workflow
 
net.sourceforge.seqware.pipeline.workflowV2 - package net.sourceforge.seqware.pipeline.workflowV2
 
net.sourceforge.seqware.pipeline.workflowV2.model - package net.sourceforge.seqware.pipeline.workflowV2.model
 
net.sourceforge.seqware.pipeline.workflowV2.pegasus - package net.sourceforge.seqware.pipeline.workflowV2.pegasus
 
net.sourceforge.seqware.pipeline.workflowV2.pegasus.object - package net.sourceforge.seqware.pipeline.workflowV2.pegasus.object
 
net.sourceforge.seqware.queryengine.backend.factory - package net.sourceforge.seqware.queryengine.backend.factory
 
net.sourceforge.seqware.queryengine.backend.factory.impl - package net.sourceforge.seqware.queryengine.backend.factory.impl
 
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
 
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
 
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
net.sourceforge.seqware.queryengine.backend.model - package net.sourceforge.seqware.queryengine.backend.model
 
net.sourceforge.seqware.queryengine.backend.store - package net.sourceforge.seqware.queryengine.backend.store
 
net.sourceforge.seqware.queryengine.backend.store.impl - package net.sourceforge.seqware.queryengine.backend.store.impl
 
net.sourceforge.seqware.queryengine.backend.util - package net.sourceforge.seqware.queryengine.backend.util
 
net.sourceforge.seqware.queryengine.backend.util.iterators - package net.sourceforge.seqware.queryengine.backend.util.iterators
 
net.sourceforge.seqware.queryengine.examples - package net.sourceforge.seqware.queryengine.examples
 
net.sourceforge.seqware.queryengine.prototypes - package net.sourceforge.seqware.queryengine.prototypes
 
net.sourceforge.seqware.queryengine.prototypes.hadoop - package net.sourceforge.seqware.queryengine.prototypes.hadoop
 
net.sourceforge.seqware.queryengine.tools.annotators - package net.sourceforge.seqware.queryengine.tools.annotators
 
net.sourceforge.seqware.queryengine.tools.exporters - package net.sourceforge.seqware.queryengine.tools.exporters
 
net.sourceforge.seqware.queryengine.tools.importers - package net.sourceforge.seqware.queryengine.tools.importers
 
net.sourceforge.seqware.queryengine.tools.importers.workers - package net.sourceforge.seqware.queryengine.tools.importers.workers
 
net.sourceforge.seqware.queryengine.tools.iterators - package net.sourceforge.seqware.queryengine.tools.iterators
 
net.sourceforge.seqware.queryengine.tools.iterators.processors - package net.sourceforge.seqware.queryengine.tools.iterators.processors
 
net.sourceforge.seqware.queryengine.tools.reporters - package net.sourceforge.seqware.queryengine.tools.reporters
 
net.sourceforge.seqware.queryengine.webservice.controller - package net.sourceforge.seqware.queryengine.webservice.controller
 
net.sourceforge.seqware.queryengine.webservice.model - package net.sourceforge.seqware.queryengine.webservice.model
 
net.sourceforge.seqware.queryengine.webservice.security - package net.sourceforge.seqware.queryengine.webservice.security
 
net.sourceforge.seqware.queryengine.webservice.util - package net.sourceforge.seqware.queryengine.webservice.util
 
net.sourceforge.seqware.queryengine.webservice.view - package net.sourceforge.seqware.queryengine.webservice.view
 
net.sourceforge.seqware.webservice.dto - package net.sourceforge.seqware.webservice.dto
 
net.sourceforge.seqware.webservice.resources - package net.sourceforge.seqware.webservice.resources
 
net.sourceforge.seqware.webservice.resources.filters - package net.sourceforge.seqware.webservice.resources.filters
 
net.sourceforge.seqware.webservice.resources.queries - package net.sourceforge.seqware.webservice.resources.queries
 
net.sourceforge.seqware.webservice.resources.tables - package net.sourceforge.seqware.webservice.resources.tables
 
net.sourceforge.solexatools - package net.sourceforge.solexatools
 
net.sourceforge.solexatools.authentication - package net.sourceforge.solexatools.authentication
 
net.sourceforge.solexatools.util - package net.sourceforge.solexatools.util
 
net.sourceforge.solexatools.validation - package net.sourceforge.solexatools.validation
 
net.sourceforge.solexatools.webapp.controller - package net.sourceforge.solexatools.webapp.controller
 
net.sourceforge.solexatools.webapp.metamodel - package net.sourceforge.solexatools.webapp.metamodel
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
newBuilder(QESupporting.AtomPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
newBuilder(QESupporting.FeatureAtomPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
newBuilder(QESupporting.FSGIDPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
newBuilder(QESupporting.SGIDPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
newBuilder(QESupporting.TagPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
newBuilder(QueryEngine.ACLPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
newBuilder(QueryEngine.AnalysisPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
newBuilder(QueryEngine.AnalysisSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
newBuilder(QueryEngine.FeatureListPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
newBuilder(QueryEngine.FeaturePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
newBuilder(QueryEngine.FeatureSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
newBuilder(QueryEngine.GroupPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
newBuilder(QueryEngine.MoleculePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
newBuilder(QueryEngine.ReferencePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
newBuilder(QueryEngine.ReferenceSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
newBuilder(QueryEngine.TagSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
newBuilder(QueryEngine.UserPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.Feature
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.FeatureList
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
Create a new AnalysisSet builder
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
Create a new AnalysisSet builder
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.interfaces.ACL
Create a new ACL builder, this is needed to add ne
newBuilder() - Static method in class com.github.seqware.queryengine.model.Tag
Create a new ACL builder
newBuilder() - Static method in class com.github.seqware.queryengine.model.User
Create a new ACL builder
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
NewSeqwareStyle - Annotation Type in net.sourceforge.seqware.pipeline.module.ann
This Annotation is used to tag a ModuleInterface.
newStudyType - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
 
newSynonym(Synonym) - Method in class com.github.seqware.queryengine.util.obo.OboFileHandlerHack
 
next() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
 
next() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
 
next() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
 
next() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
 
next() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Super method for dealing with database iterator specifics, such as closing the DB-iterator when no more data is available.
next() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
 
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
 
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
 
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
 
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
 
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
 
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
 
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
 
nextId() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
nextImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator
 
nextImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Implementation of next().
nextInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.RandomInvitationCode
 
nextInvitationCode() - Method in class net.sourceforge.solexatools.util.RandomInvitationCode
 
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
 
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Not applicable for HBase backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Not applicable for HBase backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator
 
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
Used to get the keys in this secondary table as strings (won't work for non string keys!).
nextSecondaryKey() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator
 
NO_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
NodeHtmlUtil - Class in net.sourceforge.solexatools.util
 
NodeHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.NodeHtmlUtil
 
NoExitSecurityManager - Class in net.sourceforge.seqware.common.util
Created by IntelliJ IDEA.
NoExitSecurityManager() - Constructor for class net.sourceforge.seqware.common.util.NoExitSecurityManager
 
nominallength - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
 
nominalsdev - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
 
NonPersistentStorage - Class in com.github.seqware.queryengine.impl
Doesn't really store things anywhere, just keeps it in memory.
NonPersistentStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.NonPersistentStorage
 
NonPersistentStorage.ByteTypePair - Class in com.github.seqware.queryengine.impl
 
NonPersistentStorage.ByteTypePair(byte[], Class) - Constructor for class com.github.seqware.queryengine.impl.NonPersistentStorage.ByteTypePair
 
normalizeOptions(String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner2
 
NOT_STRANDED_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
 
NotFoundException - Exception in net.sourceforge.seqware.common.err
 
NotFoundException() - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException
 
NotFoundException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException
 
NotFoundException(String) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException
 
NotFoundException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException
 
NOTIMPLEMENTED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
NS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
NULL - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
NullBeanUtils - Class in net.sourceforge.seqware.common.util
 
NullBeanUtils() - Constructor for class net.sourceforge.seqware.common.util.NullBeanUtils
 
NULLIZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
NUMBER_THREADS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
numberChannels - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
numberoflevels - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
numberofreadsperspot - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
 

O

objectCreated(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Called by Atoms when they are successfully created thus becoming dirty, and needing to be written to the database.
objectCreated(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
ObjectFactory - Class in net.sourceforge.seqware.queryengine.webservice.model
This object contains factory methods for each Java content interface and Java element interface generated in the net.sourceforge.seqware.queryengine.webservice.model package.
ObjectFactory() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: net.sourceforge.seqware.queryengine.webservice.model
objectToEntry(Object, TupleOutput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
 
objectToEntry(Object, TupleOutput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
 
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
 
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
 
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
 
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
 
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
 
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
 
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
 
OboFileHandlerHack - Class in com.github.seqware.queryengine.util.obo
The BioJava 1.8.1 package does not seem to handle Synonyms correctly, need to keep track of them separately
OboFileHandlerHack(Ontology) - Constructor for class com.github.seqware.queryengine.util.obo.OboFileHandlerHack
 
OBOImporter - Class in com.github.seqware.queryengine.system.importers
Quick and dirty OBO file importer.
OBOImporter() - Constructor for class com.github.seqware.queryengine.system.importers.OBOImporter
 
OboParser - Class in com.github.seqware.queryengine.util.obo
Copied from BioJava 1.8.1 Legacy org.biojava.ontology.io.OboParser
OboParser() - Constructor for class com.github.seqware.queryengine.util.obo.OboParser
 
OICRLdapAuthentication - Class in net.sourceforge.solexatools.authentication
This authentication plugin allows the SeqWare Portal to authenticate against the Ontario Institute for Cancer Research (OICR) LDAP server.
OICRLdapAuthentication() - Constructor for class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
 
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
OldSeqwareException - Exception in net.sourceforge.seqware.common.err
This exception wraps the old seqware exception code User: Xiaoshu Wang (xiao@renci.org) Date: 9/6/11 Time: 2:38 PM
OldSeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException
 
OldSeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException
 
OldSeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException
 
OldSeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException
 
onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
Handles the user's request to submit a new study.
onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
 
OpenInvoiceController - Class in net.sourceforge.solexatools.webapp.controller
 
OpenInvoiceController() - Constructor for class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
 
OptionParsing - Class in net.sourceforge.seqware.common.util.configtools
Created by IntelliJ IDEA.
OptionParsing() - Constructor for class net.sourceforge.seqware.common.util.configtools.OptionParsing
 
options - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
options - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
Organism - Class in net.sourceforge.seqware.common.model
 
Organism() - Constructor for class net.sourceforge.seqware.common.model.Organism
 
ORGANISM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
OrganismDAO - Interface in net.sourceforge.seqware.common.dao
 
OrganismDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
OrganismDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
 
OrganismDto - Class in net.sourceforge.seqware.webservice.dto
 
OrganismDto() - Constructor for class net.sourceforge.seqware.webservice.dto.OrganismDto
 
OrganismService - Interface in net.sourceforge.seqware.common.business
 
OrganismServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
OrganismServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
 
orientation - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
 
originalFileName - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
OUTPUT_FILE_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
outputDir - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
outputDir - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
outputFeatureInVCF(StringBuffer, Feature) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper
 
OUTPUTFILE_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
 
outputLogString(boolean, WorkflowRunReportRow, StringBuilder) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
 
outputSet - Variable in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
outputSize - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
outputZip - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
OwnerDto - Class in net.sourceforge.seqware.webservice.dto
 
OwnerDto() - Constructor for class net.sourceforge.seqware.webservice.dto.OwnerDto
 

P

packageBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
packageBundleToS3(File, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
PAD - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage
 
PAD - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
padZeros(int, int) - Static method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
PAGE_NUM - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
PAGE_NUM - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
PageInfo - Class in net.sourceforge.solexatools.util
 
PageInfo() - Constructor for class net.sourceforge.solexatools.util.PageInfo
 
PaginationUtil - Class in net.sourceforge.solexatools.util
 
PaginationUtil() - Constructor for class net.sourceforge.solexatools.util.PaginationUtil
 
paired - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
 
parameters - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
PARAMETERS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
params - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
params - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
parent - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
PARENT_SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
PARENT_SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
PARENT_SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
parentAccessionId - Variable in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.decider.Decider
 
parse_parameters() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
parse_parameters() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
 
parseCommandLine(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.StringUtils
split on the space+ only if that space has zero, or an even number of quotes in ahead of it.
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFromFile(File) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
 
parseOBO(BufferedReader, String, String) - Method in class com.github.seqware.queryengine.util.obo.OboParser
Parse a OBO file and return its content as a BioJava Ontology object
parseOption(Object, List<String>) - Static method in class net.sourceforge.seqware.common.util.configtools.OptionParsing
 
parsePegasusStatus(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
parser - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
parser - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
parseSGID(String) - Static method in class com.github.seqware.queryengine.system.Utility
Parse a timestamp-less SGID from a String representation
PASSWORD_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
pasteHtmlIntoParentNode(String, String, String, boolean) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
 
pb2m(QueryEngine.AnalysisPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisIO
 
pb2m(QueryEngine.AnalysisSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisSetIO
 
pb2m(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
 
pb2m(QueryEngine.FeatureListPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
 
pb2m(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
 
pb2m(QESupporting.FSGIDPB) - Static method in class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO
 
pb2m(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO
 
pb2m(S) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface
Convert from protein buffer object to model
pb2m(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
 
pb2m(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
 
pb2m(QESupporting.SGIDPB) - Static method in class com.github.seqware.queryengine.impl.protobufIO.SGIDIO
 
pb2m(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO
 
pb2m(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
 
pb2m(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
 
pb2m(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO
 
PegasusAbstract - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus.object
 
PegasusAbstract() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusAbstract
 
PegasusJob - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus.object
 
PegasusJob(Job) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
PegasusSeqwareModuleJob - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus.object
 
PegasusSeqwareModuleJob(Job) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusSeqwareModuleJob
 
PegasusWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus
 
PegasusWorkflowEngine(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.PegasusWorkflowEngine
 
PENDING - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
 
PENDING - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
PENDING - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
percentage - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
percentage - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
performImport(SGID, int, List<String>, String, boolean, File, List<SGID>, SGID, int, SGID, String) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter
This method does the actual work of importing given properly parsed parameters
performInMemoryRun() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
performInMemoryRun() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractMRInMemoryPlugin
 
performInMemoryRun() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractScanInMemoryPlugin
 
performVariableInit(String, String, Scan) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
This should be overridden by implementing classes with code that changes from map/reduce to map/reduce
performVariableInit(String, String, Scan) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByFilterPlugin
 
performVariableInit(String, String, Scan) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin
 
performVariableInit(String, String, Scan) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin
 
permanentBundleLocation - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
PermissionsAware - Interface in net.sourceforge.seqware.common.security
 
persist(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Start managing a Atom that has been dirtied, for example, a Atom returned from a query
persist(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
 
PERSIST_VERSION_CHAINS - Static variable in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface
 
Pfn - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus.object
 
Pfn() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Pfn
 
PHASE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
Picard - Class in net.sourceforge.seqware.pipeline.modules
 
Picard() - Constructor for class net.sourceforge.seqware.pipeline.modules.Picard
 
PileupCoverageImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
 
PileupCoverageImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.PileupCoverageImporter
 
PileupVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
PileupVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.PileupVariantImportWorker
 
Platform - Class in net.sourceforge.seqware.common.model
 
Platform() - Constructor for class net.sourceforge.seqware.common.model.Platform
 
platform - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
PlatformDAO - Interface in net.sourceforge.seqware.common.dao
 
PlatformDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
PlatformDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
 
PlatformService - Interface in net.sourceforge.seqware.common.business
 
PlatformServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
PlatformServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
 
plotStats - Class in net.sourceforge.seqware.pipeline.modules.qc
Depends on qualStat module, parse sample_stat.txt and generates boxplot sample_bxp.png for base calling scores and per base/cycle % nucleotide distribution sample_nt_distr.png Underlying script: /usr/bin/fastq_nucleotide_distribution_graph.sh /usr/bin/fastq_quality_boxplot_graph.sh Dependency: fastx_toolkits from http://hannonlab.cshl.edu/fastx_toolkit/commandline.html Expected output: sample_bxp.png & sample_nt_distr.png *
plotStats() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.plotStats
 
Plugin - Class in net.sourceforge.seqware.pipeline.plugin
 
Plugin() - Constructor for class net.sourceforge.seqware.pipeline.plugin.Plugin
 
PluginInterface - Interface in net.sourceforge.seqware.pipeline.plugin
 
PluginRunner - Class in net.sourceforge.seqware.pipeline.runner
 
PluginRunner() - Constructor for class net.sourceforge.seqware.pipeline.runner.PluginRunner
 
PLUS_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
pmi - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
position - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
PositionSeparator - Static variable in class com.github.seqware.queryengine.util.FSGID
 
POSITIVE_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
post(Representation) - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
 
post(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
 
Poster - Class in com.github.seqware.queryengine.tutorial
This is a quick and dirty sample application built on top of our API, created for Poster testing.
Poster(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.Poster
 
PosterSGE - Class in com.github.seqware.queryengine.tutorial
This is a quick and dirty application built on top of our API, created for Poster testing.
PosterSGE(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.PosterSGE
 
PosterStatCompiler - Class in com.github.seqware.queryengine.tutorial
This program compiles information generated by the Poster class.
PosterStatCompiler() - Constructor for class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
PostgresModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
An interator on top of the standard Java SQL iterator
PostgresModelIterator(ResultSet, TupleBinding, int, LargeObjectManager) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
 
PostgreSQLBulkWriterStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl
 
PostgreSQLBulkWriterStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
PostgreSQLStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl
 
PostgreSQLStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
PostgresTagModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
An interator on top of the standard Java SQL iterator
PostgresTagModelIterator(ResultSet, PostgreSQLStore) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
 
PostgresVariantModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
An interator on top of the standard Java SQL iterator
PostgresVariantModelIterator(ResultSet, PostgreSQLStore) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
 
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
 
postRun(Representation) - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
 
PRAGMA_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
PRECEDINGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
PRECEDINGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
PREDICATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
prefix - Static variable in class com.github.seqware.queryengine.model.Analysis
 
prefix - Static variable in interface com.github.seqware.queryengine.model.AnalysisSet
 
prefix - Static variable in class com.github.seqware.queryengine.model.FeatureSet
 
prefix - Static variable in interface com.github.seqware.queryengine.model.Group
 
prefix - Static variable in class com.github.seqware.queryengine.model.impl.FeatureList
 
prefix - Static variable in interface com.github.seqware.queryengine.model.Reference
 
prefix - Static variable in interface com.github.seqware.queryengine.model.ReferenceSet
 
prefix - Static variable in class com.github.seqware.queryengine.model.Tag
 
prefix - Static variable in interface com.github.seqware.queryengine.model.TagSet
 
prefix - Static variable in class com.github.seqware.queryengine.model.User
 
prepareData(WorkflowInfo, String, ArrayList<String>, Map<String, String>, boolean, ArrayList<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
prepareData(WorkflowInfo, String, ArrayList<String>, Map<String, String>, boolean, ArrayList<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.PegasusWorkflowEngine
 
prependToFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
PrepQCgenomes - Class in net.sourceforge.seqware.pipeline.modules.qc
Prepare the "QC Genomes" database from external sources.
PrepQCgenomes() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
 
PrepTranscriptDB - Class in net.sourceforge.seqware.pipeline.modules.alignment
Given a set of database tables, construct a reference set of transcripts.
PrepTranscriptDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
 
prettyPrint(String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
 
print(Writer, ReturnValue, String, boolean, FileMetadata) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Prints a line to the Excel spreadsheet.
print(String) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
print(String) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
printAndAppendtoStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
printAndAppendtoStderr(String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner
 
printAndAppendtoStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
printAndAppendtoStdout(String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner
 
printAndAppendtoString(String, String) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
 
printHeader(Writer, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Print the header of the Excel spreadsheet to file.
println(String) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
printTSVFile(Writer, boolean, List<ReturnValue>, String) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor
 
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor
 
process(Object) - Method in interface net.sourceforge.seqware.queryengine.tools.iterators.processors.ProcessorInterface
 
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor
 
processExitStatus - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
ProcessIdProcessResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
ProcessIdProcessResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource
 
ProcessIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
ProcessIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
 
Processing - Class in net.sourceforge.seqware.common.model
 
Processing() - Constructor for class net.sourceforge.seqware.common.model.Processing
 
PROCESSING - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
processing - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
PROCESSING_ALGO - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
PROCESSING_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
PROCESSING_DATE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
processing_event_to_task_group(int, int[], int[], String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
PROCESSING_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
 
PROCESSING_SWID - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
PROCESSING_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
processingAccession - Variable in class net.sourceforge.seqware.pipeline.module.Module
 
ProcessingAttribute - Class in net.sourceforge.seqware.common.model
ProcessingAttribute generated by hbm2java
ProcessingAttribute() - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute
 
ProcessingAttribute(int, Processing) - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute
 
ProcessingAttribute(int, Processing, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute
 
ProcessingAttributeDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
 
ProcessingController - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunController
ProcessingController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingController
 
ProcessingController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingController
 
ProcessingDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
ProcessingExperiments - Class in net.sourceforge.seqware.common.model
ProcessingExperiments generated by hbm2java
ProcessingExperiments() - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments
 
ProcessingExperiments(int, Processing, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments
 
ProcessingExperiments(int, Processing, Experiment, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments
 
ProcessingExperimentsDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingExperimentsDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingExperimentsDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
 
ProcessingExperimentsService - Interface in net.sourceforge.seqware.common.business
 
ProcessingExperimentsServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProcessingExperimentsServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
ProcessingIus - Class in net.sourceforge.seqware.common.model
ProcessingIus generated by hbm2java
ProcessingIus() - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus
 
ProcessingIus(int, IUS, Processing) - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus
 
ProcessingIus(int, IUS, Processing, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus
 
ProcessingIUSDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingIUSDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingIUSDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
 
ProcessingIUSService - Interface in net.sourceforge.seqware.common.business
 
ProcessingIUSServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProcessingIUSServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
ProcessingLanes - Class in net.sourceforge.seqware.common.model
ProcessingLanes generated by hbm2java
ProcessingLanes() - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes
 
ProcessingLanes(int, Processing, Lane) - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes
 
ProcessingLanes(int, Processing, Lane, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes
 
ProcessingLanesDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingLanesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingLanesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
 
ProcessingLanesService - Interface in net.sourceforge.seqware.common.business
 
ProcessingLanesServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProcessingLanesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
ProcessingList - Class in net.sourceforge.seqware.common.model.lists
 
ProcessingList() - Constructor for class net.sourceforge.seqware.common.model.lists.ProcessingList
 
ProcessingRelationship - Class in net.sourceforge.seqware.common.model
ProcessingRelationship generated by hbm2java
ProcessingRelationship() - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship
 
ProcessingRelationship(int) - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship
 
ProcessingRelationship(int, Processing, Processing, String) - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship
 
ProcessingRelationshipDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingRelationshipDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingRelationshipDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
ProcessingRelationshipService - Interface in net.sourceforge.seqware.common.business
 
ProcessingRelationshipServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProcessingRelationshipServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
ProcessingResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
ProcessingResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.ProcessingResource
 
ProcessingSamples - Class in net.sourceforge.seqware.common.model
ProcessingSamples generated by hbm2java
ProcessingSamples() - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples
 
ProcessingSamples(int, Processing, Sample) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples
 
ProcessingSamples(int, Processing, Sample, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples
 
ProcessingSamplesDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingSamplesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingSamplesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
 
ProcessingSamplesService - Interface in net.sourceforge.seqware.common.business
 
ProcessingSamplesServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProcessingSamplesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
processingsCount(Sample) - Static method in class net.sourceforge.solexatools.util.TagUtils
Returns count of the Sample related Workflow Runs.
ProcessingSequencerRuns - Class in net.sourceforge.seqware.common.model
ProcessingSequencerRuns generated by hbm2java
ProcessingSequencerRuns() - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
ProcessingSequencerRuns(int, Processing, SequencerRun) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
ProcessingSequencerRuns(int, Processing, SequencerRun, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
ProcessingSequencerRunsDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingSequencerRunsDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingSequencerRunsDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
 
ProcessingSequencerRunsService - Interface in net.sourceforge.seqware.common.business
 
ProcessingSequencerRunsServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProcessingSequencerRunsServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
ProcessingService - Interface in net.sourceforge.seqware.common.business
 
ProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
ProcessingSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
ProcessingSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
 
ProcessingStudies - Class in net.sourceforge.seqware.common.model
ProcessingStudies generated by hbm2java
ProcessingStudies() - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies
 
ProcessingStudies(int, Processing, Study) - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies
 
ProcessingStudies(int, Processing, Study, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies
 
ProcessingStudiesDAO - Interface in net.sourceforge.seqware.common.dao
 
ProcessingStudiesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProcessingStudiesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
 
ProcessingStudiesService - Interface in net.sourceforge.seqware.common.business
 
ProcessingStudiesServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProcessingStudiesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
ProcessingTaskGroup - Class in net.sourceforge.seqware.common.metadata.ProcessingTaskGroup
Standalone application to insert a new processing task group into the database.
ProcessingTaskGroup() - Constructor for class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup
 
ProcessorInterface - Interface in net.sourceforge.seqware.queryengine.tools.iterators.processors
 
ProcessResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
ProcessResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
 
processTemplate(String[], String, String, Map<String, String>, String[]) - Method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
 
ProcessTools - Class in net.sourceforge.seqware.common.util.processtools
Sleep for N seconds.
ProcessTools() - Constructor for class net.sourceforge.seqware.common.util.processtools.ProcessTools
 
PROGRAMFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
Project - Class in net.sourceforge.seqware.common.model
 
Project() - Constructor for class net.sourceforge.seqware.common.model.Project
 
ProjectDAO - Interface in net.sourceforge.seqware.common.dao
 
ProjectDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ProjectDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
 
projectid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
ProjectService - Interface in net.sourceforge.seqware.common.business
 
ProjectServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ProjectServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
 
PropagateOwnership - Class in net.sourceforge.seqware.common.hibernate
Should only be used for one query and then discarded and re-instantiated.
PropagateOwnership() - Constructor for class net.sourceforge.seqware.common.hibernate.PropagateOwnership
 
protect - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
ProtobufSerialization - Class in com.github.seqware.queryengine.impl
 
ProtobufSerialization() - Constructor for class com.github.seqware.queryengine.impl.ProtobufSerialization
 
ProtobufTransferInterface<S extends com.google.protobuf.Message,T extends Atom> - Interface in com.github.seqware.queryengine.impl.protobufIO
Interface for conversion from protein buffer auto-generated objects to model and vice versa
ProvisionDependenciesBundle - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module takes a software bundle and unzips it to the temporary directory.
ProvisionDependenciesBundle() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
 
provisionFile(String, String) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
This method was tested with: # local to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file /tmp/foo --output-dir /tmp/tmp2 # local to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file /tmp/foo --output-dir s3://seqware.bundles/dependencies/data # http to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file https://s3.amazonaws.com/seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir /tmp/tmp2 # http to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file https://s3.amazonaws.com/seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir s3://seqware.bundles/dependencies/noarch # S3 to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file s3://seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir /tmp/tmp2 # S3 to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file s3://seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir s3://seqware.bundles/dependencies/noarch
provisionFile(String, String, boolean, ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
ProvisionFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module takes one or more inputs (S3 URL, HTTP/HTTPS URL, or local file path) and copies the file to the specified output (S3 bucket URL, HTTP/HTTPS URL, or local directory path).
ProvisionFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
ProvisionFilesUtil - Class in net.sourceforge.seqware.common.util.filetools
 
ProvisionFilesUtil() - Constructor for class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Default ctor.
ProvisionFilesUtil(boolean) - Constructor for class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Set verbose mode ctor.
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
 
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
 
put(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Debug
 
put(String) - Static method in class net.sourceforge.solexatools.Debug
 
put(Object, String) - Static method in class net.sourceforge.solexatools.Debug
 
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
TODO: I think I should store each consequence as "Genome"+genomeId+"Gene"+consequence.getGeneId()
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This constructs an identifier such as: "hg18.chr12:00230.consequence.genome1212.G.ak21219", figures out the version to add e.g.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
putConsequence(Consequence, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
putConsequence(Consequence) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
putCoverage(Integer, Integer) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This constructs an identifier such as: "hg18.chr12:00230.coverage.genome1212", figures out the version to add e.g.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
putCoverage(Coverage) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
putCoverage(Coverage, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
putDestination(BufferedInputStream, String, int, String, ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
HTTP writeback currently not supported S3 uses multi-part upload which should deal with failed uploads (maybe) I'm not really dealing with failed upload recovery here...
putFeature(FeatureSet, Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This is really a pass through for putFeature(Feature feature) since the HBase backend doesn't support transactions.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This constructs an identifier such as: "hg18.chr12:00230.feature.genome1212", figures out the version to add e.g.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
putFeature(Feature, SeqWareIterator, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
putFeature(Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This constructs an identifier such as: "hg18.chr12:00230.variant.genome1212.G", figures out the version to add e.g.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This is really a pass through for putMismatch(Variant variant) since the HBase backend doesn't support transactions.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
putMismatch(Variant) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
putMismatch(Variant, SeqWareIterator, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
putModel(Database, TupleBinding, Model, Long, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
putModel(String, LocatableModel, TupleBinding, HTable, HTable, HTable, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
FIXME: what happens if something steps on this load below and creates a timestamp that exists already? may need to look at transaction support or making this syncronized (won't matter if other client on other machine overwrites this timestamp!)
putModel(String, String, String, TupleBinding, LocatableModel) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
putTag(Tag, Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
putToHttp() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Not supported yet.
putToS3(BufferedInputStream, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Copy file using reader into output.
putToS3(InputStream, String, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Copy file using reader into output.

Q

QCGenome - Class in net.sourceforge.seqware.pipeline.modules.qc
To get alignment to QC genome, currenly, human rRNA and viral genome Underlying script: sw_module_RiboAndViralAln.pl (by Sara Grimm) Necessary programs: perl path to BWA Expected output: "mock" alignment to qc genome, text file with key values
QCGenome() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
 
qcreport - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
QEMapper<KEYOUT,VALUEOUT> - Class in com.github.seqware.queryengine.plugins.hbasemr
Base mapper class used by all Query Engine plug-ins.
QEMapper() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.QEMapper
 
QEReducer<KEYIN,VALUEIN,KEYOUT,VALUEOUT> - Class in com.github.seqware.queryengine.plugins.hbasemr
Base reducer class used by all plug-ins.
QEReducer() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.QEReducer
 
QESupporting - Class in com.github.seqware.queryengine.dto
 
QESupporting.AtomPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.AtomPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.AtomPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QESupporting.FeatureAtomPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.FeatureAtomPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.FeatureAtomPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QESupporting.FSGIDPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.FSGIDPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.FSGIDPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QESupporting.SGIDPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.SGIDPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.SGIDPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QESupporting.TagPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.TagPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.TagPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
qtype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
qualFilter - Class in net.sourceforge.seqware.pipeline.modules.qc
Performing quality flitering on sequence read Underlying script: sw_module_qualFilter.pl (by Sara Grimm as base_quality_scan.pl) Necessary programs: perl Expected output: qual_filter.txt
qualFilter() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
 
qualityscorer - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
qualityscores - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
 
qualStat - Class in net.sourceforge.seqware.pipeline.modules.qc
Performing per lane based statistics Underlying script: fastx_quality_stats executable installed Dependency: fastx_quality_stats from http://hannonlab.cshl.edu/fastx_toolkit/commandline.html Currently installed at: /usr/bin/fastx_quality_stats Expected output: qual_filter.txt
qualStat() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.qualStat
 
QUERY_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
 
QueryDumperInterface - Interface in com.github.seqware.queryengine.system.exporters
This interface should be extended by a class that a developer wishes to use as input to the QueryVCFDumper.
QueryEngine - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ACLPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ACLPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ACLPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.AnalysisPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.AnalysisPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.AnalysisPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.AnalysisSetPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.AnalysisSetPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.AnalysisSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureListPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureListPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureListPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.FeaturePB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeaturePB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeaturePB.StrandPB - Enum in com.github.seqware.queryengine.dto
 
QueryEngine.FeaturePBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureSetPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureSetPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.GroupPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.GroupPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.GroupPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.MoleculePB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.MoleculePB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.MoleculePBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.ReferencePB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ReferencePB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ReferencePBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.ReferenceSetPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ReferenceSetPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ReferenceSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.TagSetPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.TagSetPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.TagSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.UserPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.UserPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.UserPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryFuture<ReturnType> - Interface in com.github.seqware.queryengine.model
This interface sketches out the result that might be returned from a asynchronous query.
QueryInterface - Interface in com.github.seqware.queryengine.model
This interface allows users to access queries that are built into the query engine, as well as install/un-install plug-ins that allow the user to perform additional annotation and/or other operations (in other words, this handles the R operations from CRUD)).
QueryInterface.Location - Enum in com.github.seqware.queryengine.model
Type of location query.
queryValues - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
 
queryValues - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
QueryVCFDumper - Class in com.github.seqware.queryengine.system.exporters
Exporter using a new interface to the parameters in order to support queries triggerable from the command-line.
QueryVCFDumper() - Constructor for class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
 
QUEUED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 

R

r - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
random - Variable in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
RandomInvitationCode - Class in net.sourceforge.seqware.common.invitation
 
RandomInvitationCode() - Constructor for class net.sourceforge.seqware.common.invitation.RandomInvitationCode
 
RandomInvitationCode - Class in net.sourceforge.solexatools.util
 
RandomInvitationCode() - Constructor for class net.sourceforge.solexatools.util.RandomInvitationCode
 
read(Kryo, Input) - Method in class com.github.seqware.queryengine.util.FSGID
 
read(Kryo, Input) - Method in class com.github.seqware.queryengine.util.SGID
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
readBases - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readclass - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
readCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readindex - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
readspec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
 
readsSupportingCallOne - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readsSupportingCallThree - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readsSupportingCallTwo - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
readTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
readtype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
rebuild() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
rebuild() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
rebuild() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
rebuild() - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Rebuild the underlying set architecture.
redirect() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig
 
REDIRECT - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
 
RedirectAspect - Class in net.sourceforge.seqware.pipeline.runner
We need to clarify that there are two issues here.
RedirectAspect() - Constructor for class net.sourceforge.seqware.pipeline.runner.RedirectAspect
 
RedirectAware - Interface in net.sourceforge.seqware.pipeline.module
This module, in conjunction with the Tag and Run annotation are used to replace the old Module with the Runner code.
reduce(FeatureSet, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
reduce(FeatureSet, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
 
reduce(FeatureSet, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin
 
reduce(S, S) - Method in interface com.github.seqware.queryengine.plugins.MapReducePlugin
Reduce implementation that takes mapped atoms and processes them.
reduceInit() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
reduceInit() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
 
reduceInit() - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin
 
reduceInit() - Method in interface com.github.seqware.queryengine.plugins.MapReducePlugin
 
Reference - Interface in com.github.seqware.queryengine.model
A reference is a particular build version such as "hg19" or "hg18".
reference - Variable in class com.github.seqware.queryengine.model.Reference.Builder
 
Reference.Builder - Class in com.github.seqware.queryengine.model
 
Reference.Builder() - Constructor for class com.github.seqware.queryengine.model.Reference.Builder
 
REFERENCE_ID_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
referencealignment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
referenceAveSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
referenceBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
referenceCache - Variable in class com.github.seqware.queryengine.util.LazyReference
 
referenceCallQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
referenceChecked - Variable in class com.github.seqware.queryengine.util.LazyReference
 
ReferenceCreator - Class in com.github.seqware.queryengine.system
Quick and dirty ReferenceCreator.
ReferenceCreator() - Constructor for class com.github.seqware.queryengine.system.ReferenceCreator
 
referenceId - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
REFERENCEID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
REFERENCEIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
ReferenceIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
ReferenceIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
 
referenceMaxSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
ReferenceSet - Interface in com.github.seqware.queryengine.model
A ReferenceSet is a collection of references which are a collection of contigs and coordinates.
ReferenceSet.Builder - Class in com.github.seqware.queryengine.model
 
ReferenceSet.Builder() - Constructor for class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
ReferenceSetIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
ReferenceSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
 
referenceSGID - Variable in class com.github.seqware.queryengine.util.LazyReference
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
 
REFNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
refRegex - Static variable in class com.github.seqware.queryengine.Constants
Regular Expression for suitable rowKeys
refresh(Atom) - Method in interface com.github.seqware.queryengine.impl.BackEndInterface
Update the obj using the latest information from the back-end
refresh(Atom) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
region - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
registerAllExtensions(ExtensionRegistry) - Static method in class com.github.seqware.queryengine.dto.QESupporting
 
registerAllExtensions(ExtensionRegistry) - Static method in class com.github.seqware.queryengine.dto.QueryEngine
 
Registration - Class in net.sourceforge.seqware.common.model
Registration
Registration() - Constructor for class net.sourceforge.seqware.common.model.Registration
 
registration - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
 
registration - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
RegistrationController - Class in net.sourceforge.solexatools.webapp.controller
 
RegistrationController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationController
 
RegistrationController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationController
 
RegistrationDAO - Interface in net.sourceforge.seqware.common.dao
 
RegistrationDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
RegistrationDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
 
RegistrationDTO - Class in net.sourceforge.seqware.common.model
 
RegistrationDTO() - Constructor for class net.sourceforge.seqware.common.model.RegistrationDTO
 
RegistrationService - Interface in net.sourceforge.seqware.common.business
 
RegistrationServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
RegistrationServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
 
RegistrationSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
RegistrationSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
 
RegistrationValidator - Class in net.sourceforge.solexatools.validation
 
RegistrationValidator() - Constructor for class net.sourceforge.solexatools.validation.RegistrationValidator
 
relativeLocation - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
release - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
releaseLock() - Method in class com.github.seqware.queryengine.system.importers.Importer
 
releaseLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated.  
releaseLock() - Method in class net.sourceforge.seqware.queryengine.tools.importers.Importer
 
releaseStore(String) - Static method in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
 
remove() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
 
remove() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
 
remove(Feature) - Method in class com.github.seqware.queryengine.model.FeatureSet
 
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.FeatureList
 
remove(T) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
remove() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
 
remove() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
 
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
remove(T) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Remove one element
remove() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Removal of subjects cannot be done implicitly from an iterator -- this method is not supported.
remove() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
 
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
 
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
 
removeAnalysisIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
removeFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
removeFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
removeFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
removeGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
RemoveIndelsAndTrim - Class in net.sourceforge.seqware.pipeline.modules.BamFilters
Purpose: Module to wrap remove_indels_and_trim script.
RemoveIndelsAndTrim() - Constructor for class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
 
removeModuleOption(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Arguments
 
removeReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
removeSelectedItemsCurrentParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
removeSelectedItemsLaunchWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
removeSequencerRun(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
RemoveSingleIndelNotOnEnds - Class in net.sourceforge.seqware.pipeline.modules.BamFilters
Purpose: Module to wrap remove_indels_and_trim script.
RemoveSingleIndelNotOnEnds() - Constructor for class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
 
removeStudy(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
removeTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
removeTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
removeTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
removeUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
removeWorkflowRun(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
removeWorkflowRunRunning(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
replace(String, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.StringUtils
 
replace(String, Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.StringUtils
 
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor
 
report() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor
 
report(Object) - Method in interface net.sourceforge.seqware.queryengine.tools.iterators.processors.ProcessorInterface
 
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor
 
reportCardSingle - Class in net.sourceforge.seqware.pipeline.modules.quantification
Generating report card on RNAseq against Microarray - Agilent 244k array.
reportCardSingle() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
 
reportException(ImportWorker) - Method in class com.github.seqware.queryengine.system.importers.FeatureImporter
 
ReportTest - Class in net.sourceforge.seqware.pipeline.tools
 
ReportTest() - Constructor for class net.sourceforge.seqware.pipeline.tools.ReportTest
 
ReportTest.TestThread - Class in net.sourceforge.seqware.pipeline.tools
 
ReportTest.TestThread() - Constructor for class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CachedTagResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.ConsequenceResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CoverageResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CoveragesResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.FileResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GeneReportResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.LiveTagResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.MismatchesResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.MismatchResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.ProcessingResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.TagResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.TemplateResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.VersionResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowRunStatusResource
 
requireRegistration(HttpServletRequest, HttpServletResponse) - Static method in class net.sourceforge.solexatools.Security
 
rerunWorkflowRun(List<String>, List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Returns true only if there are more files to run than have been run on any workflow so far, or if the filesToRun have different filepaths than those that have been run before.
resetCompletedChildren() - Method in class net.sourceforge.seqware.common.model.Processing
 
resetRunningChildren() - Method in class net.sourceforge.seqware.common.model.Processing
 
RESUBMITTED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
 
ret - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
ret - Variable in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
ret - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
RETURNEDHELPMSG - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
ReturnValue - Class in net.sourceforge.seqware.common.module
Return values > 0 are errors that will cause the runner to exit.
ReturnValue() - Constructor for class net.sourceforge.seqware.common.module.ReturnValue
 
ReturnValue(int) - Constructor for class net.sourceforge.seqware.common.module.ReturnValue
 
ReturnValue(String, String, int) - Constructor for class net.sourceforge.seqware.common.module.ReturnValue
 
returnValue - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
ReturnValue.ExitStatus - Enum in net.sourceforge.seqware.common.module
 
ReturnValueList - Class in net.sourceforge.seqware.common.model.lists
 
ReturnValueList() - Constructor for class net.sourceforge.seqware.common.model.lists.ReturnValueList
 
RIGHTS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
root - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
RootSampleResource - Class in net.sourceforge.seqware.webservice.resources.tables
This resource should pull back only samples without parents
RootSampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
 
ROWKEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
ROWS_PER_PAGE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
ROWS_PER_PAGE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
RPNStack - Class in com.github.seqware.queryengine.kernel
A stack of arguments and operations in Reverse Polish Notation (RPN, http://en.wikipedia.org/wiki/Reverse_Polish_notation).
RPNStack(Object...) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack
 
RPNStack.Constant - Class in com.github.seqware.queryengine.kernel
 
RPNStack.Constant(Object) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.Constant
 
RPNStack.FeatureAttribute - Class in com.github.seqware.queryengine.kernel
Represents attributes of features that are passed as parameter.
RPNStack.FeatureAttribute(String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.FeatureAttribute
 
RPNStack.Operation - Enum in com.github.seqware.queryengine.kernel
Operations for combining query constraints.
RPNStack.Parameter - Class in com.github.seqware.queryengine.kernel
 
RPNStack.Parameter(String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
RPNStack.TagHierarchicalOccurrence - Class in com.github.seqware.queryengine.kernel
Represents tags whose occurrence is tested -- including the tags children!
RPNStack.TagHierarchicalOccurrence(String, String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagHierarchicalOccurrence
 
RPNStack.TagOccurrence - Class in com.github.seqware.queryengine.kernel
Represents tags whose occurrence is probed.
RPNStack.TagOccurrence(String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagOccurrence
 
RPNStack.TagValuePresence - Class in com.github.seqware.queryengine.kernel
Represents tag/value pairs that should be present.
RPNStack.TagValuePresence(String, Tag.ValueType, Object) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
run() - Method in class com.github.seqware.queryengine.system.importers.workers.GFF3VariantImportWorker
 
run() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
run() - Method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
 
run() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
 
run(String[]) - Method in class net.sourceforge.seqware.pipeline.runner.PluginRunner
 
run(String[]) - Method in class net.sourceforge.seqware.pipeline.runner.Runner
 
run() - Method in class net.sourceforge.seqware.pipeline.runner.Runner2
 
run() - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.BedFeatureImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.GFF3VariantImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.PileupVariantImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.U87LargeDeletionVariantImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.U87TranslocationVariantImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.VCFVariantImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.VenterGenomeVariantImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.WatsonGenomeVariantImportWorker
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.YanHuangGenomeVariantImportWorker
 
run - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunSet
 
runattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES
 
runattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runCenter - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
 
runCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
 
runCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
 
runCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
A simple command runner that captures the return value of the program.
runDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runFile - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runInSessionCalculations() - Method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
 
runlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS
 
runlinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runMain(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Interface for mock-testing
runMain(String[]) - Static method in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Interface for mock-testing
Runner - Class in net.sourceforge.seqware.pipeline.runner
 
Runner() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner
 
Runner.Keys - Interface in net.sourceforge.seqware.pipeline.runner
 
Runner2 - Class in net.sourceforge.seqware.pipeline.runner
This is a new Runner class that is designed (hopefuly) to replace the current Runner class.
Runner2() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner2
 
Runner2.ModuleConfig - Class in net.sourceforge.seqware.pipeline.runner
This class is used to configure the instantiating of a module
Runner2.ModuleConfig() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner2.ModuleConfig
 
RUNNERERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
RunnerParams - Class in net.sourceforge.seqware.pipeline.runner
This class is used to pass information from the Runner class to the Configuration class, which can instantiate the module and setup the bean.
RunnerParams() - Constructor for class net.sourceforge.seqware.pipeline.runner.RunnerParams
 
RunnerParams.Bean - Interface in net.sourceforge.seqware.pipeline.runner
 
RUNNING - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
 
RUNNING - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun
 
RUNNING - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
RUNNING - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
runref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
RunSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunSet
 
runStartTstmp - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
runStopTstmp - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
RUNTIMEEXCEPTION - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
RunTools - Class in net.sourceforge.seqware.common.util.runtools
 
RunTools() - Constructor for class net.sourceforge.seqware.common.util.runtools.RunTools
 
RunType - Class in net.sourceforge.seqware.queryengine.webservice.model
A Run contains the sequencing results from a particular run on a sequencing instrument.
RunType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
RunType.DATABLOCK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.DATABLOCK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
RunType.DATABLOCK.FILES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.DATABLOCK.FILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES
 
RunType.DATABLOCK.FILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.DATABLOCK.FILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
 
RunType.EXPERIMENTREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.EXPERIMENTREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
 
RunType.RUNATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES
 
RunType.RUNATTRIBUTES.RUNATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNATTRIBUTES.RUNATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
 
RunType.RUNLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS
 
RunType.RUNLINKS.RUNLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
 
RunType.RUNLINKS.RUNLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
 
RunType.RUNLINKS.RUNLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
 
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
 
RunWorkflowResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
RunWorkflowResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource
 

S

S3CreateFileURLs - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module simply lists files at the S3 URL you provide and creates temporary URLs that can be shared with others.
S3CreateFileURLs() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
S3DeleteFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module simply lists files at the S3 URL you provide.
S3DeleteFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
S3ListFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module simply lists files at the S3 URL you provide.
S3ListFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
Sample - Class in net.sourceforge.seqware.common.model
 
Sample() - Constructor for class net.sourceforge.seqware.common.model.Sample
 
sample - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleSet
 
SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
SAMPLE_CHILD - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
SAMPLE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
 
SAMPLE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
 
SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
SampleAttribute - Class in net.sourceforge.seqware.common.model
SampleAttribute generated by hbm2java
SampleAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
 
SampleAttribute(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
 
SampleAttribute(int, Sample, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
 
sampleattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES
 
sampleAttributeAsDto(SampleAttribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
 
SampleAttributeDAO - Interface in net.sourceforge.seqware.common.dao
 
SampleAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
SampleAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
 
sampleattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
SampleController - Class in net.sourceforge.solexatools.webapp.controller
SampleController
SampleController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController
 
SampleController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController
 
SampleDAO - Interface in net.sourceforge.seqware.common.dao
 
SampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
SampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
sampledescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
SampleDetailsLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
 
SampleDetailsLineItem(SequencerRun, Lane, IUS) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
 
SampleDetailsWorkflowLineItems - Class in net.sourceforge.solexatools.webapp.metamodel
 
SampleDetailsWorkflowLineItems(Sample) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
 
SampleDetailsWorkflowLineItems(Processing) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
 
sampleId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
 
sampleId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
 
SampleIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
SampleIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource
 
SampleIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
 
SampleIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
 
SampleIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
SampleIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
 
SampleLink - Class in net.sourceforge.seqware.common.model
SampleLink generated by hbm2java
SampleLink() - Constructor for class net.sourceforge.seqware.common.model.SampleLink
 
SampleLink(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink
 
SampleLink(int, Sample, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink
 
samplelink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS
 
SampleLinkDAO - Interface in net.sourceforge.seqware.common.dao
 
SampleLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
SampleLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
 
samplelinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
SampleList - Class in net.sourceforge.seqware.common.model.lists
 
SampleList() - Constructor for class net.sourceforge.seqware.common.model.lists.SampleList
 
samplename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
samplepoolref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
sampleRef - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
 
sampleref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
sampleRef - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
 
SampleReportDAO - Interface in net.sourceforge.seqware.common.dao
 
SampleReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
SampleReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
SampleReportRow - Class in net.sourceforge.seqware.common.model
 
SampleReportRow() - Constructor for class net.sourceforge.seqware.common.model.SampleReportRow
 
SampleReportService - Interface in net.sourceforge.seqware.common.business
 
SampleReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
SampleReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
SampleResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
SampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleResource
 
SampleSearch - Class in net.sourceforge.seqware.common.model
A search for samples that match a given list of attributes.
SampleSearch() - Constructor for class net.sourceforge.seqware.common.model.SampleSearch
 
SampleSearchAttribute - Class in net.sourceforge.seqware.common.model
Attributes that are part of a sample search.
SampleSearchAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
SampleSearchDAO - Interface in net.sourceforge.seqware.common.dao
 
SampleSearchDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
SampleSearchDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
 
SampleSearchDto - Class in net.sourceforge.seqware.webservice.dto
 
SampleSearchDto() - Constructor for class net.sourceforge.seqware.webservice.dto.SampleSearchDto
 
SampleSearchService - Interface in net.sourceforge.seqware.common.business
 
SampleSearchServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
SampleSearchServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
 
SampleService - Interface in net.sourceforge.seqware.common.business
 
SampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
SampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
SampleSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleSet
 
SampleSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
SampleSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
SampleType - Class in net.sourceforge.seqware.queryengine.webservice.model
A Sample defines an isolate of sequenceable material upon which sequencing experiments can be based.
SampleType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
SampleType.MEMBERS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.MEMBERS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS
 
SampleType.MEMBERS.MEMBER - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.MEMBERS.MEMBER() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
 
SampleType.SAMPLEATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLEATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES
 
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
 
SampleType.SAMPLELINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLELINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS
 
SampleType.SAMPLELINKS.SAMPLELINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
 
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
 
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
 
SampleType.SAMPLENAME - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLENAME() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
 
SampleValidator - Class in net.sourceforge.solexatools.validation
 
SampleValidator() - Constructor for class net.sourceforge.solexatools.validation.SampleValidator
 
SampleWorkflowRunsController - Class in net.sourceforge.solexatools.webapp.controller
 
SampleWorkflowRunsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
 
SamTools - Class in net.sourceforge.seqware.pipeline.modules
FIXME: if creating pileup requres a .fai file!
SamTools() - Constructor for class net.sourceforge.seqware.pipeline.modules.SamTools
 
saveAscInSession(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
 
saveAscInSession(HttpServletRequest, String) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
saveFile(MultipartFile, String, Registration) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
saveFile(MultipartFile, String, Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
saveFileForIus(int, int, FileMetadata) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
saveFileForIus(int, int, FileMetadata) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
saveFileForIus(int, int, FileMetadata) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
saveFileForIus(int, int, FileMetadata) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
SaveOpenNodeController - Class in net.sourceforge.solexatools.webapp.controller
 
SaveOpenNodeController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
saveSelectedWorkflowParamValue(HttpServletRequest, Integer, String) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
scan(T, S) - Method in interface com.github.seqware.queryengine.plugins.ScanPlugin
Scanner implementation that processes atoms and aggregates results in a new set.
ScanPlugin<T extends Atom,S extends MolSetInterface> - Interface in com.github.seqware.queryengine.plugins
An abstracted map-reduce interface.
scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
This method just needs a sw_accession value from the workflow table and an ini file(s) in order to schedule a workflow.
scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
 
scheduleWorkflowRun(int, String, String, String, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
schema - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
 
schema - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
 
score - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
SCORE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
SEARCH_CASE_SENSITIVE - Static variable in class net.sourceforge.solexatools.webapp.controller.SearchController
 
SearchController - Class in net.sourceforge.solexatools.webapp.controller
 
SearchController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchController
 
SearchResultsController - Class in net.sourceforge.solexatools.webapp.controller
 
SearchResultsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsController
 
SearchResultsListController - Class in net.sourceforge.solexatools.webapp.controller
 
SearchResultsListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
SECONDARY_INDEX - Static variable in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
 
SECONDARY_INDEX_HACK - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
SECONDARY_INDEX_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
SecondaryCursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
 
SecondaryCursorIterator(SecondaryCursor, TupleBinding, boolean) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
Used to iterate over an entire secondary table with or without duplicates reported
SecondaryCursorIterator(SecondaryCursor, DatabaseEntry, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
Used to search the secondary table with only duplicates reported back
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
sector - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
Security - Class in net.sourceforge.solexatools
 
Security() - Constructor for class net.sourceforge.solexatools.Security
 
SELECTED_FILES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
SELECTED_NODES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
SELECTED_VALUES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
selectExperimentNode(List<String>, Study) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
SelectInputController - Class in net.sourceforge.solexatools.webapp.controller
 
SelectInputController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController
 
SelectInputController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController
 
SelectInputListController - Class in net.sourceforge.solexatools.webapp.controller
 
SelectInputListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
selectIUSNode(List<String>, Sample) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
selectProcessingNode(List<String>, WorkflowRun) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
selectProcessingNode(List<String>, Processing) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
selectProcessingNode(List<String>, Lane) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
selectProcessingNode(List<String>, IUS) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
selectSampleNode(List<String>, Experiment) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
selectStudyNode(List<String>, List<Study>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
selectWorkflowRunNode(List<String>, List<WorkflowRun>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
separateFiles(List<ReturnValue>, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
SEPARATOR - Static variable in class com.github.seqware.queryengine.impl.StorageInterface
 
SEPARATOR - Static variable in class com.github.seqware.queryengine.model.Tag
 
SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
 
SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
 
SEQ_RUN_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
SEQUENCER_RUN_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
SEQUENCER_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
SEQUENCER_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
SEQUENCER_RUN_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
SEQUENCER_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
 
SequencerRun - Class in net.sourceforge.seqware.common.model
 
SequencerRun() - Constructor for class net.sourceforge.seqware.common.model.SequencerRun
 
SequencerRunAttribute - Class in net.sourceforge.seqware.common.model
SequencerRunAttribute generated by Morgan Taschuk
SequencerRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
SequencerRunAttribute(int, SequencerRunWizardDTO) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
SequencerRunAttribute(int, SequencerRunWizardDTO, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
SequencerRunController - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunController
SequencerRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController
 
SequencerRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController
 
SequencerRunControllerDTO - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunController
SequencerRunControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
 
SequencerRunControllerDTO(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
 
SequencerRunDAO - Interface in net.sourceforge.seqware.common.dao
 
SequencerRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
SequencerRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
SequencerRunDTO - Class in net.sourceforge.seqware.common.model
 
SequencerRunDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunDTO
 
SequencerRunHtmlUtil - Class in net.sourceforge.solexatools.util
 
SequencerRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
SequencerRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
SequencerRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource
 
SequencerRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
SequencerRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
 
SequencerRunList - Class in net.sourceforge.seqware.common.model.lists
 
SequencerRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.SequencerRunList
 
SequencerRunListController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
SequencerRunListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
 
SequencerRunListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
 
SequencerRunListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
SequencerRunReport - Class in net.sourceforge.seqware.common.hibernate
 
SequencerRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport
 
SequencerRunReport.Row - Class in net.sourceforge.seqware.common.hibernate
 
SequencerRunReport.Row(Date, String, String, String, String, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
SequencerRunReporter - Class in net.sourceforge.seqware.pipeline.plugins
 
SequencerRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
 
SequencerRunReportId - Class in net.sourceforge.seqware.common.model
 
SequencerRunReportId() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunReportId
 
SequencerRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
SequencerRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource
 
SequencerRunReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
SequencerRunReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
 
SequencerRunReportTableController - Class in net.sourceforge.solexatools.webapp.controller
 
SequencerRunReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
SequencerRunResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
SequencerRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
 
SequencerRunService - Interface in net.sourceforge.seqware.common.business
 
SequencerRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
SequencerRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
SequencerRunSetupController - Class in net.sourceforge.solexatools.webapp.controller
SequencingRunSetupController
SequencerRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
 
SequencerRunSetupControllerDTO - Class in net.sourceforge.solexatools.webapp.controller
SequencingRunSetupController
SequencerRunSetupControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
 
SequencerRunValidator - Class in net.sourceforge.solexatools.validation
 
SequencerRunValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunValidator
 
SequencerRunWizardController - Class in net.sourceforge.solexatools.webapp.controller
 
SequencerRunWizardController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
SequencerRunWizardController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
SequencerRunWizardDTO - Class in net.sourceforge.seqware.common.model
 
SequencerRunWizardDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
 
SequencerRunWizardSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
SequencerRunWizardSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
 
SequencerRunWizardValidator - Class in net.sourceforge.solexatools.validation
 
SequencerRunWizardValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
 
sequencers - Static variable in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
sequencers - Static variable in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
sequencers - Static variable in class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
sequencespace - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
 
sequencingprotocol - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
SEQWARE_SETTINGS_PROPERTY - Static variable in class com.github.seqware.queryengine.common.ConfigTools
 
SEQWARE_SETTINGS_PROPERTY - Static variable in class net.sourceforge.seqware.common.util.configtools.ConfigTools
 
SeqwareAccessionIDResource - Class in net.sourceforge.seqware.webservice.resources
 
SeqwareAccessionIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
 
SeqwareAccessionResource - Class in net.sourceforge.seqware.webservice.resources
 
SeqwareAccessionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
 
SeqWareBase - Class in net.sourceforge.seqware.queryengine.backend.util
 
SeqWareBase() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
 
SeqWareCursor - Class in net.sourceforge.seqware.queryengine.backend.util
 
SeqWareCursor() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareCursor
 
SeqwareException - Exception in net.sourceforge.seqware.common.err
Created by IntelliJ IDEA.
SeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
 
SeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
 
SeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
 
SeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
 
SeqWareException - Exception in net.sourceforge.seqware.queryengine.backend.util
 
SeqWareException() - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException
 
SeqWareException(String) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException
 
SeqWareException(Throwable) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException
 
SeqWareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException
 
SeqwareExitCode - Class in net.sourceforge.seqware.common.err
Created by IntelliJ IDEA.
SeqwareExitCode() - Constructor for class net.sourceforge.seqware.common.err.SeqwareExitCode
 
SeqWareIterable<T> - Interface in com.github.seqware.queryengine.util
All SeqWare iterable collections should be easily countable too
SeqWareIterator<T> - Class in com.github.seqware.queryengine.util
Iterator implementation that deals with database iterators that require explicit closing.
SeqWareIterator() - Constructor for class com.github.seqware.queryengine.util.SeqWareIterator
 
SeqWareIterator - Interface in net.sourceforge.seqware.queryengine.backend.util
 
SeqwareModuleJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
SeqwareModuleJob(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SeqwareModuleJob
 
SeqwareModuleJob(String, boolean) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SeqwareModuleJob
 
SeqwareModuleJob(String, Module) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SeqwareModuleJob
 
SeqwareModuleJob(String, Module, boolean) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SeqwareModuleJob
 
SeqWareSettings - Class in net.sourceforge.seqware.queryengine.backend.util
 
SeqWareSettings() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
SeqWareVerifier - Class in net.sourceforge.seqware.queryengine.webservice.security
 
SeqWareVerifier() - Constructor for class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
 
SeqWareWebServiceApplication - Class in net.sourceforge.seqware.queryengine.webservice.controller
 
SeqWareWebServiceApplication() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
 
SeqWareWebServiceApplication.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller
http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
SeqWareWebServiceApplication.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
 
SeqWareWebServiceApplication.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
 
SeqWareWebServiceApplicationVersion - Class in net.sourceforge.seqware.queryengine.webservice.controller
 
SeqWareWebServiceApplicationVersion() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
 
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller
http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
 
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
 
SeqWareWebServiceMain - Class in net.sourceforge.seqware.queryengine.webservice.controller
 
SERIALIZATIONCONSTANT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
SERIALIZATIONCONSTANT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
SerializationInterface - Interface in com.github.seqware.queryengine.impl
This simply extracts the serialization of bytes[] to atoms and vice versa.
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.ApacheSerialization
 
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.KryoSerialization
 
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization
 
serialize(Atom) - Method in interface com.github.seqware.queryengine.impl.SerializationInterface
Given an atom, get back an array of bytes
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.impl.StorageInterface
Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomsToTarget(Atom...) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
 
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
 
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.StorageInterface
Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Adag
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Arguments
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusAbstract
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusSeqwareModuleJob
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Pfn
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
set - Variable in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
set(T) - Method in class com.github.seqware.queryengine.util.LazyReference
Set the lazy reference of the object with an actual object.
setABISOLID(ExperimentType.PLATFORM.ABISOLID) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Sets the value of the abisolid property.
setAbstractStr(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setABUNDANCEMEASUREMENT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the abundancemeasurement property.
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Organism
 
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the accession property.
setAcl(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
setAcl(QueryEngine.ACLPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
setACTIONS(SubmissionType.ACTIONS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the actions property.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareFile
 
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareLane
 
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareSample
 
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
setAdapters(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
setADAPTERSPEC(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Sets the value of the adapterspec property.
setADD(SubmissionType.ACTIONS.ACTION.ADD) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the add property.
setAddedSurcharge(Double) - Method in class net.sourceforge.seqware.common.model.Expense
 
setAdditionalAttribute(String, Feature.AdditionalAttributeType) - Method in class com.github.seqware.queryengine.model.Feature
Sets an additional attribute not covered by GVF.
setAdhoctagset(SGID) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setAgent(String) - Method in class net.sourceforge.seqware.common.model.Expense
 
setAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setAlgorithm(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setAlgorithm(String) - Method in class net.sourceforge.seqware.pipeline.module.Module
 
setAlgorithm(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setAlias(String) - Method in class net.sourceforge.seqware.common.model.IUS
 
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the alias property.
setAlign(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setAllItems(String) - Method in class net.sourceforge.solexatools.util.PageInfo
 
setANALYSISATTRIBUTES(AnalysisType.ANALYSISATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysisattributes property.
setAnalysisCenter(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysisCenter property.
setANALYSISFILES(AnalysisType.ANALYSISFILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysisfiles property.
setAnalysisIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setAnalysisIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setANALYSISLINKS(AnalysisType.ANALYSISLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysislinks property.
setAnalysisPluginACL(ACL, AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setAnalysisSetACL(ACL, AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setANALYSISTYPE(AnalysisType.ANALYSISTYPE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysistype property.
setAnonymizedName(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setANONYMIZEDNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Sets the value of the anonymizedname property.
setApplicationContext(ApplicationContext) - Method in class net.sourceforge.seqware.pipeline.runner.Runner2
 
setArch(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
setArgs(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
 
setAsText(String) - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
setAtom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setAtom(QESupporting.FeatureAtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setAtom(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
setAttribute(String, String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setAttributes(Map<String, String>) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
 
setBackendTimestamp(Date) - Method in class com.github.seqware.queryengine.util.SGID
 
setBarcode(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setBarcodeSeqence(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Sets the value of the barcodeSeqence property.
setBaseCaller(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setBASECALLER(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
Sets the value of the basecaller property.
setBASECALLS(ExperimentType.PROCESSING.BASECALLS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
Sets the value of the basecalls property.
setBaseCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setBASECOORD(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the basecoord property.
setBaseDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setBaseIniFile(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setBaseQualities(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setBatch_size(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setBinSize(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setBinSize(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setBlockCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setBlockSizes(int[]) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setBlockStarts(int[]) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setBrokerName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the brokerName property.
setCacheSize(long) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setCalledBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setCalledBaseCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setCalledBaseCountForward(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setCalledBaseCountReverse(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setCallOne(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setCallTwo(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setCascade(boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
setCell(List<String>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
 
setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setCenterName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the centerName property.
setCENTERNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the centername property.
setCenterName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the centerName property.
setCenterProjectName(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setCENTERPROJECTNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the centerprojectname property.
setChecksum(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Sets the value of the checksum property.
setChecksumMethod(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Sets the value of the checksumMethod property.
setChildren(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setChildren(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample
 
setChildrenUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setClassesDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setClientNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setCode(String) - Method in class net.sourceforge.seqware.common.model.Organism
 
setCode(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
 
setCodingStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setCodingStop(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setCOLORMATRIX(ExperimentType.PLATFORM.ABISOLID.COLORMATRIX) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Sets the value of the colormatrix property.
setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setCOLORMATRIXCODE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Sets the value of the colormatrixcode property.
setCommand(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setCommand(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setCommand(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setCommand(String, boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setCOMMONNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Sets the value of the commonname property.
setCompleted(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setCompressed(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setCompressed(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setComputeReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.decider.Decider
 
setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
setConfigPath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setConfirmEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
 
setConfirmPassword(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
 
setConnectionString(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setConsensusAveSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setConsensusBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setConsensusCallQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setConsensusMaxSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setConstructionProtocol(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setCONTACTS(SubmissionType.CONTACTS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the contacts property.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
 
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setContig(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
setCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
setCountFile(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
 
setCoverage(HashMap<Integer, Integer>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
setCreateConsequenceAnnotationDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setCreateCoverageDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setCreated(Date) - Method in class net.sourceforge.seqware.common.model.SampleSearch
 
setCreateDbSNPAnnotationDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setCreateMismatchDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Project
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile
 
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane
 
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample
 
setCriteria(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
 
setCurrentSelectedFiles(HttpServletRequest, List<File>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
setCurrentSelectedNodes(HttpServletRequest, List<String>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
setCurrentWorkingDir(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setCwd(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setCycleCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setCYCLECOORD(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the cyclecoord property.
setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setCYCLECOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Sets the value of the cyclecount property.
setCYCLECOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Sets the value of the cyclecount property.
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setCYCLESEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Sets the value of the cyclesequence property.
setData(ArrayList) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
setDatabase(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setDataDecryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Sets data decryption key.
setDataEncryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Sets data encryption key.
setDate(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setDate(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
setDax(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setDaysUntilDue(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setDb(Connection) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
setDb(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
setDb(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
 
setDb(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
 
setDb(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
 
setDb(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
 
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
Sets the value of the db property.
setDbmd(DatabaseMetaData) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
setDebug(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
 
setDecodeMethod(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
setDefaultValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setDENOVOASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the denovoassembly property.
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Expense
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.File
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.IUS
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Platform
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Project
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.StudyType
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setDescription(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setDescription(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setDescription(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the description property.
setDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the description property.
setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setDESCRIPTOR(StudyType.DESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the descriptor property.
setDESIGN(ExperimentType.DESIGN) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the design property.
setDESIGNDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Sets the value of the designdescription property.
setDibase(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
Sets the value of the dibase property.
setDisplay(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setDisplay(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.FileType
 
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
setDisplayName(String) - Method in class net.sourceforge.solexatools.util.SummaryLine
 
setDisplayValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
 
setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
 
setEarliestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Set the value of earliestDate.
setEmail(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
 
setEmailAddress(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setEmailAddress(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.Registration
 
setEnd(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setEndDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setEndPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo
 
setEntityUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
setENTREZLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Sets the value of the entrezlink property.
setENTREZLINK(ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
Sets the value of the entrezlink property.
setENTREZLINK(RunType.RUNLINKS.RUNLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
Sets the value of the entrezlink property.
setENTREZLINK(SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
Sets the value of the entrezlink property.
setENTREZLINK(StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
Sets the value of the entrezlink property.
setErrorCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setExistingStudyType(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
Sets the value of the existingStudyType property.
setExistingType(StudyType) - Method in class net.sourceforge.seqware.common.model.Study
 
setExistingTypeInt(Integer) - Method in class net.sourceforge.seqware.common.model.Study
 
setExitCode(int) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
 
setExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
 
setExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setExpectedBaseCall(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setEXPECTEDBASECALL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the expectedbasecall property.
setExpectedNumberReads(Long) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpectedNumberReads(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the expectedNumberReads property.
setExpectedNumberRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpectedNumberRuns(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the expectedNumberRuns property.
setExpectedNumberSpots(Long) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpectedNumberSpots(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the expectedNumberSpots property.
setExpectedNumReads(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
 
setExpectedNumRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
 
setExpectedNumSpots(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
 
setExpenseId(Integer) - Method in class net.sourceforge.seqware.common.model.Expense
 
setExpenses(Set<Expense>) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setExpenseType(String) - Method in class net.sourceforge.seqware.common.model.Expense
 
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.Sample
 
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
setExperiment(Experiment, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setExperimentAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
setExperimentAttributes(Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setEXPERIMENTATTRIBUTES(ExperimentType.EXPERIMENTATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the experimentattributes property.
setExperimentDAO(ExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
Sets a private member variable with an instance of an implementation of ExperimentDAO.
setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
setExperimentId(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExperimentLibraryDesign(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
 
setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
 
setExperimentLibraryDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setExperimentLinkId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
setExperimentLinks(Set<ExperimentLink>) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setEXPERIMENTLINKS(ExperimentType.EXPERIMENTLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the experimentlinks property.
setEXPERIMENTREF(AnalysisType.PARENT.EXPERIMENTREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the experimentref property.
setEXPERIMENTREF(RunType.EXPERIMENTREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the experimentref property.
setExperiments(Set<Experiment>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setExperiments(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.model.Study
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
 
setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
 
setExperimentSpotDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
 
setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
 
setExperimentSpotDesignReadSpecId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setExperimentSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setExpiryTime(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
setExpLibDesignDesc(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpLibDesignName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpLibDesignProtocol(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpLibDesignSelection(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpLibDesignSource(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpLibDesignStrategy(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpSpotDesignAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpSpotDesignReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExpSpotDesignTagSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setExtension(String) - Method in class net.sourceforge.seqware.common.model.FileType
 
setExternalId(String) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setExternalSerializationVersion(int) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
setFactoryBackendType(SWQEFactory.Model_Type, SWQEFactory.Storage_Type, SWQEFactory.Serialization_Type) - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Used only by testing to override the back-end type
setFailed(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setFastqConvNum(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setFastqConvNum(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setFeatureACL(ACL, Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setFeatures(int, QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
setFeatures(int, QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
setFeatures(int, QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setFeatures(int, QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setFeatureSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setFeatureSet(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setFeatureSetACL(ACL, Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setFeatureSetID(SGID) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setFeatureSetIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setFeatureSetIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setFile(MultipartFile) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setFile(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
setFile(File) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setFile(File) - Method in class net.sourceforge.seqware.common.model.ShareFile
 
setFile(File) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
setFileAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
setFileAttributes(Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.model.File
 
setFileDAO(FileDAO) - Method in interface net.sourceforge.seqware.common.business.FileService
 
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setFileForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setFileForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setFileForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setFileId(Integer) - Method in class net.sourceforge.seqware.common.model.File
 
setFileMetaType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setFileMetaType(String) - Method in class net.sourceforge.solexatools.util.SummaryLine
 
setFilename(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
Sets the value of the filename property.
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
Sets the value of the filename property.
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Sets the value of the filename property.
setFileOne(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.File
 
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setFilePath(File) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setFilePath(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setFilePath(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
setFileReportDAO(FileReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
setFiles(Set<File>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setFiles(List<File>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setFiles(ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setFILES(RunType.DATABLOCK.FILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the files property.
setFILES(SubmissionType.FILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the files property.
setFiles(List<File>) - Method in class net.sourceforge.solexatools.util.SummaryLine
 
setFiles_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setFilesArray(ArrayList<File>) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
setFileService(FileService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
setFileSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setFileTwo(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setFileTwoURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setFileType(FileType) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.File
 
setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setFiletype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
Sets the value of the filetype property.
setFiletype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
Sets the value of the filetype property.
setFileTypeDAO(FileTypeDAO) - Method in interface net.sourceforge.seqware.common.business.FileTypeService
 
setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
Sets a private member variable with an instance of an implementation of FileTypeDAO.
setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileType
 
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
 
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
 
setFileUploadService(FileUploadService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setFileURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setFileURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setFinalDestination(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
setFinalized(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setFinishedTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Expense
 
setFirstName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setFirstName(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setFirstName(String) - Method in class net.sourceforge.seqware.common.model.Registration
 
setFirstName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
 
setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setFLOWCOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Sets the value of the flowcount property.
setFLOWCOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Sets the value of the flowcount property.
setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setFLOWSEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Sets the value of the flowsequence property.
setFLOWSEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Sets the value of the flowsequence property.
setFolderStore(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setFolderStore(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setForceRunAll(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setFormatCode(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the formatCode property.
setFrame(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setFriendlyRowkey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Analysis.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder
Set a friendly rowKey for the atom to be built.
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Reference.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.util.FSGID
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.util.SGID
 
setFullyPaid(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setFuzzyStartPositionMax(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setFuzzyStopPositionMin(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setGeneChr(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setGeneId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setGeneId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setGenomeId(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setGenomicSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setGroup(Group) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
Set the group permissions
setGroup(SGID) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
Set the SGID for the group permissions
setGroup(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setGroupACL(ACL, Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setGrp(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setGrp(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setGrps(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setGrps(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setHandle(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the handle property.
setHasProcessingFile(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setHeader(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setHELICOS(ExperimentType.PLATFORM.HELICOS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Sets the value of the helicos property.
setHOLD(SubmissionType.ACTIONS.ACTION.HOLD) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the hold property.
setHoldForPeriod(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Sets the value of the holdForPeriod property.
setHoldUntilDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Sets the value of the holdUntilDate property.
setHost(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setHost(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setHost(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setHtml(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setHtml(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setHtml(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setHYBRIDASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the hybridassembly property.
setId(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setId(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
setId(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
 
setId(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
 
setId(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
 
setId(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
 
setId(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
 
setId(String) - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface
 
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.StringId
 
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
Sets the value of the id property.
setIdentitySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
setILLUMINA(ExperimentType.PLATFORM.ILLUMINA) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Sets the value of the illumina property.
setIncludeCoverage(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setIncludeCoverage(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setIncludeIndels(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setIncludeIndels(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setIncludeIndels(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setIncludeSNV(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setIncludeSNV(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setIncludeSNVs(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setIndividualName(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setInfo(String) - Method in class net.sourceforge.solexatools.util.PageInfo
 
setInformOnError(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Sets the value of the informOnError property.
setInformOnStatus(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Sets the value of the informOnStatus property.
setIniFile(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setInput(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setInput(String) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setInputAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setInputFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
setInstalled(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
setInstitution(String) - Method in class net.sourceforge.seqware.common.model.Registration
 
setInstitution(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
 
setInstrumentModel(String) - Method in class net.sourceforge.seqware.common.model.Platform
 
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Sets the value of the instrumentmodel property.
setInstrumentModel(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the instrumentModel property.
setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setInstrumentName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the instrumentName property.
setInvitationCode(String) - Method in class net.sourceforge.seqware.common.model.Registration
 
setInvoice(Invoice) - Method in class net.sourceforge.seqware.common.model.Expense
 
setInvoiceDAO(InvoiceDAO) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
Sets a private member variable with an instance of an implementation of InvoiceDAO.
setInvoiceDAO(InvoiceDAO) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
setInvoiceId(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
 
setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
 
setIsEnd(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo
 
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
 
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
 
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing
 
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
 
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Study
 
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.File
 
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
 
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
 
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing
 
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
 
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Study
 
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setIsStart(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo
 
setItemRgb(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSLink
 
setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Lane
 
setIUS(Set<IUS>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Sample
 
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
setIus(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setIus(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
setIusAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
setIusAttributes(Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.model.IUS
 
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Sets a private member variable with an instance of an implementation of IUSDAO.
setIUSDAO(IUSDAO) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
setIusId(Integer) - Method in class net.sourceforge.seqware.common.model.IUS
 
setIusLinkId(int) - Method in class net.sourceforge.seqware.common.model.IUSLink
 
setIusLinks(Set<IUSLink>) - Method in class net.sourceforge.seqware.common.model.IUS
 
setIusService(IUSService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setIusSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setJdbcTemplate(SimpleJdbcTemplate) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect
 
setJobContext() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
setJobContext() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusSeqwareModuleJob
 
setJobs(Collection<Job>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
setJoinDevelopersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
 
setJoinUsersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
 
setKey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setKey(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder
' Should not be called outside of the back-end
setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
 
setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
 
setKeyIndex(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setKeyvalues(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
 
setLabel(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
 
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
Sets the value of the label property.
setLabName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the labName property.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.IUS
 
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneLink
 
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ShareLane
 
setLane1(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLane2(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLane3(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLane4(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLane5(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLane6(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLane7(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLane8(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLane_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setLaneAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
setLaneAttributes(Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.model.Lane
 
setLaneCount(int) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
 
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Sets a private member variable with an instance of an implementation of LaneDAO.
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Sets a private member variable with an instance of an implementation of LaneDAO.
setLaneDAO(LaneDAO) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
setLaneForSequrncerRun(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setLaneForStudy(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setLaneId(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
 
setLaneIndex(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
 
setLaneLinkId(int) - Method in class net.sourceforge.seqware.common.model.LaneLink
 
setLaneLinks(Set<LaneLink>) - Method in class net.sourceforge.seqware.common.model.Lane
 
setLanes(Set<Lane>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample
 
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setLaneService(LaneService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.validation.LaneValidator
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
setLanesForView(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample
 
setLaneSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setLastName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setLastName(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setLastName(String) - Method in class net.sourceforge.seqware.common.model.Registration
 
setLastName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
 
setLatestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Set the value of latestDate.
setLayout(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setLeastSigBits(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
setLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setLIBRARYCONSTRUCTIONPROTOCOL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the libraryconstructionprotocol property.
setLIBRARYDESCRIPTOR(ExperimentType.DESIGN.LIBRARYDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Sets the value of the librarydescriptor property.
setLibraryId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
 
setLIBRARYLAYOUT(ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the librarylayout property.
setLIBRARYNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the libraryname property.
setLibrarySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
setLIBRARYSELECTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the libraryselection property.
setLibrarySelectionDAO(LibrarySelectionDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
Sets a private member variable with an instance of an implementation of StudyTypeDAO.
setLibrarySelectionDAO(LibrarySelectionDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
 
setLibrarySelectionId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
setLibraryService(LibraryService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setLIBRARYSOURCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the librarysource property.
setLibrarySourceDAO(LibrarySourceDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
Sets a private member variable with an instance of an implementation of StudyTypeDAO.
setLibrarySourceDAO(LibrarySourceDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
 
setLibrarySourceId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
setLIBRARYSTRATEGY(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the librarystrategy property.
setLibraryStrategyDAO(LibraryStrategyDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
Sets a private member variable with an instance of an implementation of StudyTypeDAO.
setLibraryStrategyDAO(LibraryStrategyDAO) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
 
setLibraryStrategyId(Integer) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
setLibraryType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
setLIMSAdmin(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
 
setList(List<Experiment>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
 
setList(List<File>) - Method in class net.sourceforge.seqware.common.model.lists.FileList
 
setList(List<IUS>) - Method in class net.sourceforge.seqware.common.model.lists.IUSList
 
setList(List<Lane>) - Method in class net.sourceforge.seqware.common.model.lists.LaneList
 
setList(List<Processing>) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
 
setList(List<ReturnValue>) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
 
setList(List<Sample>) - Method in class net.sourceforge.seqware.common.model.lists.SampleList
 
setList(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
 
setList(List<Study>) - Method in class net.sourceforge.seqware.common.model.lists.StudyList
 
setList(List<Workflow>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
 
setList(List<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
 
setList(List<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
 
setList(Collection<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
 
setList(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
 
setLS454(ExperimentType.PLATFORM.LS454) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Sets the value of the ls454 property.
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Analysis.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Set the model manager for this Atom
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder
Set a manager for this Atom
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Reference.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setMaxCoverage(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setMaxCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setMaxCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setMaximumMappingQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setMaximumMappingQuality(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setMaxLockers(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setMaxLockObjects(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setMaxLocks(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setMd5sum(String) - Method in class net.sourceforge.seqware.common.model.File
 
setMd5sum(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
setMEMBERS(SampleType.MEMBERS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the members property.
setMemReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.decider.Decider
 
setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Lets you set the metadata object
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.module.Module
 
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Lets you set the metadata object
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
setMetadataOverridden(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setMetadataWriteback(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setMetaType(String) - Method in class net.sourceforge.seqware.common.model.File
 
setMetaType(String) - Method in class net.sourceforge.seqware.common.model.FileType
 
setMetaType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setMetaType(List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setMetaType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
setMinCoverage(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setMinCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setMinCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setMinObservations(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setMinObservationsPerStrand(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setMinPercent(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setMinSnpQuality(float) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setMinSnpQuality(float) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setMinSNVPhred(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setMismatchAAChangeBlosumScore(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMismatchAminoAcidChange(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMismatchChr(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMismatchCodonChange(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMismatchCodonPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMismatchId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMismatchStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMismatchStop(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMismatchType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMODIFY(SubmissionType.ACTIONS.ACTION.MODIFY) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the modify property.
setModuleParameter(List<String>) - Method in class net.sourceforge.seqware.pipeline.runner.Runner2
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setMostSigBits(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
setMULTIPLIER(double) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Sets the value of the multiplier property.
setMutatedGenomicSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setMutatedTranslatedSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.Reference.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
setName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setName(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setName(String) - Method in class net.sourceforge.seqware.common.model.IUS
 
setName(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
setName(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
setName(String) - Method in class net.sourceforge.seqware.common.model.Organism
 
setName(String) - Method in class net.sourceforge.seqware.common.model.Platform
 
setName(String) - Method in class net.sourceforge.seqware.common.model.Project
 
setName(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setName(String) - Method in class net.sourceforge.seqware.common.model.StudyType
 
setName(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setName(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
setName(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the name property.
setName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Sets the value of the name property.
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
 
setName(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setNameNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
 
setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
setNcbiTaxId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism
 
setNcbiTaxonomyId(Integer) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
 
setNetworkReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setNewStudyType(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
Sets the value of the newStudyType property.
setNewType(String) - Method in class net.sourceforge.seqware.common.model.Study
 
SetNodeIdInSession - Class in net.sourceforge.solexatools.util
 
SetNodeIdInSession() - Constructor for class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setNominalLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setNOMINALLENGTH(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Sets the value of the nominallength property.
setNominalSdev(Long) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setNOMINALSDEV(Double) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Sets the value of the nominalsdev property.
setNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Sets the value of the notes property.
setNotRunned(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setNumberChannels(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the numberChannels property.
setNUMBEROFLEVELS(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Sets the value of the numberoflevels property.
setNUMBEROFREADSPERSPOT(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Sets the value of the numberofreadsperspot property.
setOffspringProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setOrganism(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setOrganism(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
 
setOrganism(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
setOrganism(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setOrganism(Organism) - Method in class net.sourceforge.seqware.common.model.Sample
 
setOrganism(OrganismDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setOrganismDAO(OrganismDAO) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
Sets a private member variable with an instance of an implementation of StudyTypeDAO.
setOrganismDAO(OrganismDAO) - Method in interface net.sourceforge.seqware.common.business.OrganismService
 
setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism
 
setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
 
setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
 
setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
setORIENTATION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Sets the value of the orientation property.
setOriginalFileName(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
setOs(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setOutputFilename(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
setOutputFilename(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setOutputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
setOwner(SGID) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
Set the SGID for the owner permissions
setOwner(User) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
Set the user permissions
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.File
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.IUS
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Lane
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Processing
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Sample
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Study
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setOwner(OwnerDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setOwnerId(Integer) - Method in class net.sourceforge.seqware.common.model.Project
 
setPage(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
setPaidAmount(Double) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setPAIRED(ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
Sets the value of the paired property.
setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setPairedOrientation(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setParameter(RPNStack.Parameter, Object) - Method in class com.github.seqware.queryengine.kernel.RPNStack
Sets a parameter to a concrete value.
setParameters(ByteString) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
setParameters(List<Object>) - Method in class com.github.seqware.queryengine.model.Analysis.Builder
Set the group for the current Atom
setParameters(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setParameters(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setParameters(List<String>) - Method in class net.sourceforge.seqware.pipeline.module.Module
This method doesn't just copy the list, it actually parses through the list and looks for values that start with " or ' and then attempts to merge other parameters separated by space until an param ending with " or ' is found.
setParameters(List<String>) - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
 
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.decider.Decider
 
setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
 
setParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryLine
 
setPARENT(AnalysisType.PARENT) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the parent property.
setParentAccessionId(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
setParentProcessingAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
setParentProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
setParents(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setParents(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample
 
setParentUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setParentWorkflowAccessions(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setPassword(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setPassword(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setPassword(String) - Method in class net.sourceforge.seqware.common.model.Registration
 
setPassword(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setPasswordHint(String) - Method in class net.sourceforge.seqware.common.model.Registration
 
setPasswordWithoutHash(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setPathToFirstFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setPathToSecondFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setPayee(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
 
setPending(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setPermanentBundleLocation(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setPermBundleLocation(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setPermissions(ACL) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
setPermissions(ACL) - Method in interface com.github.seqware.queryengine.model.interfaces.ACLable
Set permissions for this
setPfn(Pfn) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
setPhase(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setPhase(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setPLATFORM(ExperimentType.PLATFORM) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the platform property.
setPlatformDAO(PlatformDAO) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
Sets a private member variable with an instance of an implementation of StudyTypeDAO.
setPlatformDAO(PlatformDAO) - Method in interface net.sourceforge.seqware.common.business.PlatformService
 
setPlatformId(Integer) - Method in class net.sourceforge.seqware.common.model.Platform
 
setPlatformInt(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setPlatformInt(int) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setPlatformService(PlatformService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
 
setPlugin(AnalysisPluginInterface) - Method in class com.github.seqware.queryengine.model.Analysis.Builder
 
setPlugin(AnalysisPluginInterface) - Method in class com.github.seqware.queryengine.model.Analysis
Set up the analysis plug-in
setPlugin(AnalysisPluginInterface) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
 
setPmi(Importer) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setPmi(Importer) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setPostgresqlPersistenceStrategy(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setPragma(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setPragma(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setPrecedingID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setPrecedingID(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setPrecedingID(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setPrecedingID(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setPrecedingSGID(SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Used in back-end to set previous version without side-effects
setPrecedingVersion(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setPrecedingVersion(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setPrecedingVersion(QueryEngine.AnalysisPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
setPrecedingVersion(QueryEngine.AnalysisPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
 
setPrecedingVersion(QueryEngine.AnalysisSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setPrecedingVersion(QueryEngine.AnalysisSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
 
setPrecedingVersion(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setPrecedingVersion(QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setPrecedingVersion(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setPrecedingVersion(QueryEngine.FeatureSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setPrecedingVersion(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setPrecedingVersion(QueryEngine.GroupPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setPrecedingVersion(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setPrecedingVersion(QueryEngine.ReferencePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setPrecedingVersion(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setPrecedingVersion(QueryEngine.ReferenceSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setPrecedingVersion(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setPrecedingVersion(QueryEngine.TagSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setPrecedingVersion(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setPrecedingVersion(QueryEngine.UserPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setPrecedingVersion(T) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
setPrecedingVersion(T) - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable
Explicitly set the previous version of a Atom.
setPredicate(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setPredicate(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setPricePerUnit(Double) - Method in class net.sourceforge.seqware.common.model.Expense
 
setPrivate(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setProcCountInfo(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
setProcCountInfo(List<SequencerRun>) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
setProcess(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setProcessedCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setProcessExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
 
setProcessExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
setPROCESSING(ExperimentType.PROCESSING) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the processing property.
setProcessingAccession(int) - Method in class net.sourceforge.seqware.pipeline.module.Module
 
setProcessingAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
setProcessingAttributes(Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setProcessingByChildId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
 
setProcessingByParentId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
 
setProcessingCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Sets a private member variable with an instance of an implementation of ProcessingDAO.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
Sets a private member variable with an instance of an implementation of ProcessingDAO.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
setProcessingDAO(ProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
 
setProcessingExperimentsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
setProcessingExperimentsService(ProcessingExperimentsService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setProcessingForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setProcessingForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setProcessingForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setProcessingForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setProcessingId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
 
setProcessingIUSDAO(ProcessingIUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
setProcessingIUSDAO(ProcessingIUSDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
 
setProcessingIusId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
setProcessingIusService(ProcessingIUSService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setProcessingLanesDAO(ProcessingLanesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
setProcessingLanesDAO(ProcessingLanesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
 
setProcessingLaneService(ProcessingLanesService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setProcessingLanesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
 
setProcessingRelationshipId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
 
setProcessingRelationshipService(ProcessingRelationshipService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.File
 
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.IUS
 
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane
 
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Sample
 
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Study
 
setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
 
setProcessingSamplesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
setProcessingSamplesService(ProcessingSamplesService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
 
setProcessingSequencerRunService(ProcessingSequencerRunsService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setProcessingSequencerRunsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
setProcessingsForView(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane
 
setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
 
setProcessingStudiesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
setProcessingStudiesService(ProcessingStudiesService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setProjectDAO(ProjectDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
Sets a private member variable with an instance of an implementation of ProjectDAO.
setProjectDAO(ProjectDAO) - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Project
 
setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Study
 
setPROJECTID(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the projectid property.
setPROTECT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the protect property.
setPublic(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setQCREPORT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the qcreport property.
setQtype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Sets the value of the qtype property.
setQualityMultiplier(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setQualityNumberOfLevels(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setQualityScorer(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setQUALITYSCORER(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Sets the value of the qualityscorer property.
setQualityType(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setReadBases(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReadClass(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setREADCLASS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the readclass property.
setReadCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReader(BufferedReader) - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
 
setReadIndex(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setREADINDEX(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the readindex property.
setReadLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setReadOnly(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setReadSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
setReadSpecs(SortedSet<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
setReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
setReadsSupportingCallOne(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReadsSupportingCallThree(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReadsSupportingCallTwo(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReadType(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
setREADTYPE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the readtype property.
setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setReference(Reference) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setReference(Reference) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
setReference(Reference) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
setReferenceACL(ACL, Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setREFERENCEALIGNMENT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the referencealignment property.
setReferenceAveSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReferenceBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReferenceCallQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReferenceID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setReferenceID(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
setReferenceId(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setReferenceIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setReferenceIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setReferenceMaxSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setReferenceSetACL(ACL, ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setRefName(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
Sets the value of the refname property.
setRegion(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the region property.
setRegions(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setRegions(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareFile
 
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareLane
 
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareSample
 
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
setRegistrationDAO(RegistrationDAO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
Sets a private member variable with an instance of an implementation of RegistrationDAO.
setRegistrationDAO(RegistrationDAO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
 
setRegistrationId(Integer) - Method in class net.sourceforge.seqware.common.model.Registration
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setRegistrationService(RegistrationService) - Static method in class net.sourceforge.seqware.webservice.resources.BasicResource
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
 
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
setRelationship(String) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
 
setRelativeLocation(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setRELEASE(SubmissionType.ACTIONS.ACTION.RELEASE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the release property.
setRequireFiles(boolean) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
setReturnIds(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setReturnValue(ReturnValue) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
 
setReturnValue(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setRights(int, boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setRights(boolean[]) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
 
setRights(List<Boolean>) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
 
setRootProcessingName(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setRootProcessingSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setRootSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
setRowKey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setRows(List<Flexigrid.Cells>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
setRUNATTRIBUTES(RunType.RUNATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runattributes property.
setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setRunCenter(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runCenter property.
setRunDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runDate property.
setRunFile(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runFile property.
setRUNLINKS(RunType.RUNLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runlinks property.
setRUNREF(AnalysisType.PARENT.RUNREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the runref property.
setRunStartTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
 
setRunStartTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setRunStopTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
 
setRunStopTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.IUS
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.Lane
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleLink
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleSearch
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ShareSample
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setSample_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setSampleAttributeId(int) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
setSampleAttributes(Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.model.Sample
 
setSAMPLEATTRIBUTES(SampleType.SAMPLEATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the sampleattributes property.
setSampleCode(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Sets a private member variable with an instance of an implementation of SampleDAO.
setSampleDAO(SampleDAO) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
setSAMPLEDESCRIPTOR(ExperimentType.DESIGN.SAMPLEDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Sets the value of the sampledescriptor property.
setSampleForStudy(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setSampleForWorkflowRun(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setSampleForWorkflowRunRunning(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
 
setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setSampleId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
Sets the value of the sampleId property.
setSampleId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Sets the value of the sampleId property.
setSampleId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
 
setSampleLinkId(int) - Method in class net.sourceforge.seqware.common.model.SampleLink
 
setSampleLinks(Set<SampleLink>) - Method in class net.sourceforge.seqware.common.model.Sample
 
setSAMPLELINKS(SampleType.SAMPLELINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the samplelinks property.
setSAMPLENAME(SampleType.SAMPLENAME) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the samplename property.
setSAMPLEPOOLREF(AnalysisType.PARENT.SAMPLEPOOLREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the samplepoolref property.
setSampleRef(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
Sets the value of the sampleRef property.
setSAMPLEREF(AnalysisType.PARENT.SAMPLEREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the sampleref property.
setSampleRef(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Sets the value of the sampleRef property.
setSampleReportDAO(SampleReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
setSampleReportService(SampleReportService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setSamples(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Project
 
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setSampleSearch(SampleSearch) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
setSampleSearchAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
setSampleSearchAttributes(Set<SampleSearchAttribute>) - Method in class net.sourceforge.seqware.common.model.SampleSearch
 
setSampleSearchId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearch
 
setSampleService(SampleService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.validation.SampleValidator
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
 
setSampleSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setSampleType(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setSampleUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
 
setSchema(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Sets the value of the schema property.
setSchema(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Sets the value of the schema property.
setScore(double) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setScore(Double) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setScore(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setSector(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the sector property.
setSelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setSender(MailSender) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
 
setSeqid(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setSequencer_run_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.Lane
 
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
setSequencerRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setSequencerRunAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
setSequencerRunAttributes(Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Sets a private member variable with an instance of an implementation of SequencerRunDAO.
setSequencerRunDAO(SequencerRunDAO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setSequencerRuns(Set<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
 
setSequencerRunSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setSequencerRunValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
setSequencerRunWizardDTO(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
setSequencerRunWizardValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
 
setSequenceSpace(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setSEQUENCESPACE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
Sets the value of the sequencespace property.
setSEQUENCINGPROTOCOL(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the sequencingprotocol property.
setSeqwareRevision(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setSeqwareVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setSerializationConstant(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setSerializationConstant(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setServer(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setSessionFactory(SessionFactory) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setSettings(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setSettings(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
setSettings(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
setSettings(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
setSETTINGS_MAP(Map<String, String>) - Static method in class com.github.seqware.queryengine.Constants
Set the settings map, overriding hard-coded values for our constants.
setSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setSgid(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setSgid(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setSgid(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setSgid(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setSGID(SGID) - Method in class com.github.seqware.queryengine.util.LazyReference
Set the SGID of the object to be lazy referenced
setSharedStudies(SortedSet<ShareStudy>) - Method in class net.sourceforge.seqware.common.model.Study
 
setSharedWorkflowRuns(SortedSet<ShareWorkflowRun>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setShareExperimentDAO(ShareExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
setShareExperimentDAO(ShareExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
setShareExperimentId(int) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
setShareFileDAO(ShareFileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
setShareFileDAO(ShareFileDAO) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
setShareFileId(int) - Method in class net.sourceforge.seqware.common.model.ShareFile
 
setShareLaneDAO(ShareLaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
setShareLaneDAO(ShareLaneDAO) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
setShareLaneId(int) - Method in class net.sourceforge.seqware.common.model.ShareLane
 
setShareProcessingDAO(ShareProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
setShareProcessingDAO(ShareProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
setShareProcessingId(int) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
setShareSampleDAO(ShareSampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
setShareSampleDAO(ShareSampleDAO) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
setShareSampleId(int) - Method in class net.sourceforge.seqware.common.model.ShareSample
 
setShareStudyDAO(ShareStudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
Sets a private member variable with an instance of an implementation of ShareStudyDAO.
setShareStudyDAO(ShareStudyDAO) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
setShareStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
Sets a private member variable with an instance of an implementation of ShareWorkflowRunDAO.
setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
setShareWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
 
setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
setSINGLE(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
Sets the value of the single property.
setSite(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Pfn
 
setSize(Long) - Method in class net.sourceforge.seqware.common.model.File
 
setSize(Long) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
 
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
 
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
 
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setSkip(Boolean) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setSkipTxt(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setSortable(boolean) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setSortKeySample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setSource(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setSource(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setSource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setSource(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Sets the value of the source property.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Sets the value of the source property.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Sets the value of the source property.
setSPOTDECODEMETHOD(Long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
Sets the value of the spotdecodemethod property.
setSPOTDECODESPEC(ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
Sets the value of the spotdecodespec property.
setSPOTDESCRIPTOR(ExperimentType.DESIGN.SPOTDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Sets the value of the spotdescriptor property.
setSpotDesignReadSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setSql(Statement) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
setStart(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setStart(long) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setStart(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
setStartDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setStartPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo
 
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
 
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setState(CreateUpdateManager.State) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
setState(String) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setStats(HashMap) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Project
 
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setStatus(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setStatusCmd(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setStatusCounts(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
setStatuses(String[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setStderr(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setStdErr(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setStderr(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware
 
setStderrFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module
Added by Xiaoshu Wang: Setter for the file that will be used to redirect stderr
setStdout(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setStdOut(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setStdout(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware
 
setStdoutFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module
 
setStop(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setStop(long) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setStop(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
 
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setStore(Store) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setStore(BerkeleyDBStore) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
setStore(Store) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
setStoreType(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setStrand(QueryEngine.FeaturePB.StrandPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setStrand(Feature.Strand) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setStrand(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setStrand(char) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
setStrExpectedNumberReads(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setStrExpectedNumberRuns(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setStrExpectedNumReads(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setStrExpectedNumRuns(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setStrLaneCount(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
 
setStrRefLane(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setStrStartURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setStrStartURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setStudies(Set<Study>) - Method in class net.sourceforge.seqware.common.model.Processing
 
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.FileReportRow
 
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
 
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyLink
 
setStudy(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setSTUDYABSTRACT(JAXBElement<String>) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the studyabstract property.
setStudyAttributeId(int) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
setStudyAttributes(Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.model.Study
 
setSTUDYATTRIBUTES(StudyType.STUDYATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the studyattributes property.
setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Sets a private member variable with an instance of an implementation of StudyDAO.
setStudyDAO(StudyDAO) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
setSTUDYDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the studydescription property.
setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.Study
 
setStudyLinkId(int) - Method in class net.sourceforge.seqware.common.model.StudyLink
 
setStudyLinks(Set<StudyLink>) - Method in class net.sourceforge.seqware.common.model.Study
 
setSTUDYLINKS(StudyType.STUDYLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the studylinks property.
setSTUDYREF(AnalysisType.PARENT.STUDYREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the studyref property.
setSTUDYREF(ExperimentType.STUDYREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the studyref property.
setStudyService(StudyService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.validation.StudyValidator
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
setStudySwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setSTUDYTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the studytitle property.
setSTUDYTYPE(StudyType.DESCRIPTOR.STUDYTYPE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the studytype property.
setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
Sets a private member variable with an instance of an implementation of StudyTypeDAO.
setStudyTypeDAO(StudyTypeDAO) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
 
setStudyTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.StudyType
 
setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
 
setSubmissionComment(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the submissionComment property.
setSubmissionDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the submissionDate property.
setSubmissionId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the submissionId property.
setSum(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
setSummaryLines(List<SummaryLine>) - Method in class net.sourceforge.solexatools.util.SummaryData
 
setSUPPRESS(SubmissionType.ACTIONS.ACTION.SUPPRESS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the suppress property.
setSvType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setSwa(Integer) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Expense
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.File
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.IUS
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareFile
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareLane
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareSample
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Study
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setTag(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.IUS
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
setTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag
 
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Sets the value of the tag property.
setTagACL(ACL, Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setTags(String) - Method in class net.sourceforge.seqware.common.model.Lane
 
setTags(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setTags(HashMap<String, String>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
 
setTags(HashMap<String, String>) - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface
 
setTags(HashMap<String, String>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setTagSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setTagSet(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setTagSet(TagSet) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setTagSet(SGID) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setTagSet(SGID) - Method in class com.github.seqware.queryengine.model.Tag
Set the TagSet for this particular tag, should not be called outside of the back-end.
setTagSet(TagSet) - Method in class com.github.seqware.queryengine.model.Tag
Set the TagSet for this particular tag, should not be called outside of the back-end.
setTagSetACL(ACL, TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setTagSetIDs(List<SGID>) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setTagSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
setTagSpecIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setTagSpecIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
Sets the value of the target property.
setTaskGroup(boolean) - Method in class net.sourceforge.seqware.common.model.Processing
 
setTAXONID(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Sets the value of the taxonid property.
setTemplate(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setTemplate(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setTemplateFile(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
setTemplatePath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setTemplateType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
setTest(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setTestCmd(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setThickEnd(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setThickStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setThreadCount(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
setTimestamp(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
setTimestamp(Date) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Set the clientTimestamp, this should never be called outside of the backend
setTimeTaken(String) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
SETTINGSFILENOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
setTissSource(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Study
 
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the title property.
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the title property.
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the title property.
setTombstone(boolean) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setTombstone(boolean) - Method in class com.github.seqware.queryengine.util.FSGID
Back-end method for Features stored within high capacity featuresets
setTotal(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
 
setTotalDataBlocks(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the totalDataBlocks property.
setTotalPrice(Double) - Method in class net.sourceforge.seqware.common.model.Expense
 
setTotalReads(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the totalReads property.
setTotalSpots(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the totalSpots property.
setTotalUnits(Double) - Method in class net.sourceforge.seqware.common.model.Expense
 
setTRANSCRIPTASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the transcriptassembly property.
setTranscriptId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
setTRANSCRIPTSEQUENCING(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the transcriptsequencing property.
setTranslatedSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
setTranslocationDestinationContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setTranslocationDestinationStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setTranslocationDestinationStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setTranslocationType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setTTL(long, boolean) - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet
 
setTTL(int, boolean) - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet
 
setTTL(long, boolean) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
setTTL(int, boolean) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
setTTL(long, boolean) - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Convenience method to set the expiry time
setTTL(int, boolean) - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Convenience method to set the expiry time for roughly hours ahead
setType(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setType(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setType(String) - Method in class net.sourceforge.seqware.common.model.File
 
setType(String) - Method in class net.sourceforge.seqware.common.model.Sample
 
setType(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
setType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
setType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
setType(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
 
setTypeNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setUnit(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
setUnit(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
setUnits(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
setUnits(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
setUnits(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
setUnits(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
setUnits(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
setUnits(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
setUnits(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Sets the value of the units property.
setup(Mapper<ImmutableBytesWritable, Result, KEYOUT, VALUEOUT>.Context) - Method in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper
 
setup(String) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker
 
setup(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
setup(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
setup(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
This allows you to search for different types of data in the metadb not just query engine databases
setup() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
setup(ArrayList) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Project
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
 
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile
 
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane
 
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
 
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample
 
setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.File
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
 
setUrl(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
 
setUrl(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setUrl(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setUrl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.Pfn
 
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
Sets the value of the url property.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
 
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
 
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
 
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
 
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.File
 
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setURLLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Sets the value of the urllink property.
setURLLINK(ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
Sets the value of the urllink property.
setURLLINK(RunType.RUNLINKS.RUNLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
Sets the value of the urllink property.
setURLLINK(SampleType.SAMPLELINKS.SAMPLELINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
Sets the value of the urllink property.
setURLLINK(StudyType.STUDYLINKS.STUDYLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
Sets the value of the urllink property.
setUrlString(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
setUseOneURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setUser(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setUser(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setUsername(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setUsername(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
setUsers(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setUsers(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setUseTwoURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence
 
setUseURL(Boolean) - Method in class net.sourceforge.seqware.common.business.UploadFile
 
setUuid(UUID) - Method in class com.github.seqware.queryengine.util.SGID
 
setVALIDATE(SubmissionType.ACTIONS.ACTION.VALIDATE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the validate property.
setValidationReportService(ValidationReportService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
 
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
 
setValue(Object) - Method in class com.github.seqware.queryengine.model.Tag.Builder
Set the value to one of ValueType
setValue(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
 
setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
 
setValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag
 
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Sets the value of the value property.
setValue(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Sets the value of the value property.
setValue(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
 
setValues(SortedSet<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setVBytes(ByteString) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVDouble(double) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVerbose(boolean) - Static method in class com.github.seqware.queryengine.common.Log
override the log4j.properties
setVerbose(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Enable class verbose mode.
setVerbose(boolean) - Static method in class net.sourceforge.seqware.common.util.Log
override the log4j.properties
setVersion(String) - Method in class net.sourceforge.seqware.common.model.Processing
 
setVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setVersion(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
setVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
setVFloat(float) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVInteger(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVisibleParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryData
 
setVLong(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVSGIDRef(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVSGIDRef(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVString(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setWfRuns(WorkflowRun[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
setWidth(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setWithHasFile(SortedSet<Experiment>) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
setWithHasFile(Set<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService
 
setWithHasFile(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
setWithHasFile(Set<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
setWithHasFile(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
setWithHasFile(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
setWithHasFile(Set<Processing>) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
setWithHasFile(Set<Processing>, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
setWithHasFile(Integer, SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
setWithHasFile(SortedSet<IUS>) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
setWithHasFile(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
setWithHasFile(Set<Processing>) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
setWithHasFile(Set<Processing>, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
setWithHasFile(Integer, SortedSet<Sample>) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
setWorkerName(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
setWorkerName(String) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
 
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
 
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
 
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusAbstract
 
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowContext
 
setWorkflowAccession(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setWorkflowAccession(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setWorkflowAccessionsToCheck(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setWorkflowAttributes(Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setWorkflowDAO(WorkflowDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
Sets a private member variable with an instance of an implementation of WorkflowDAO.
setWorkflowDAO(WorkflowDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
setWorkflowDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setWorkflowId(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setWorkflowParam(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
setWorkflowParamDAO(WorkflowParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
setWorkflowParamDAO(WorkflowParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
setWorkflowParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
 
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
 
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
 
setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
setWorkflowParamValueId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
 
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
 
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Expense
 
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing
 
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
setWorkflowRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setWorkflowRunAttributes(Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setWorkflowRunByAncestorWorkflowRunId(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing
 
setWorkflowRunDAO(WorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
Sets a private member variable with an instance of an implementation of WorkflowRunDAO.
setWorkflowRunDAO(WorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
 
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
Sets a private member variable with an instance of an implementation of WorkflowRunDAO.
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
setWorkflowRunParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
setWorkflowRunParams(SortedSet<WorkflowRunParam>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setWorkflowRunProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
setWorkflowRunRunning(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setWorkflowRunRunningWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.IUS
 
setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Lane
 
setWorkflowRuns(SortedSet<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
 
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
 
setWorkflowRunWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setWorkflows(ArrayList<WorkflowInfo>) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
 
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
 
setWorkflowSqwVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setXREFLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Sets the value of the xreflink property.
setZygosity(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SGID - Class in com.github.seqware.queryengine.util
A wrapper for our eventual choice of globally unique primary key which may or may not be UUIDs.
SGID() - Constructor for class com.github.seqware.queryengine.util.SGID
Create a new SGID
SGID(String) - Constructor for class com.github.seqware.queryengine.util.SGID
Generate a SGID that can look up things given only a rowKey.
SGID(SGID) - Constructor for class com.github.seqware.queryengine.util.SGID
Clone a given SGID
SGID(long, long, long, String) - Constructor for class com.github.seqware.queryengine.util.SGID
Back-end constructor, create a fully functional SGID
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
SGIDIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
SGIDIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.SGIDIO
 
SGIDIterable<T extends Atom> - Class in com.github.seqware.queryengine.util
A bit of a hack class, allows us to have getCount as well as iterable
SGIDIterable(Iterable<SGID>, Class<T>) - Constructor for class com.github.seqware.queryengine.util.SGIDIterable
 
SGIDIterable.SGIDIterator - Class in com.github.seqware.queryengine.util
 
SGIDIterable.SGIDIterator() - Constructor for class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
 
SGIDTB - Class in com.github.seqware.queryengine.impl.tuplebinderIO
 
SGIDTB() - Constructor for class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
 
ShareExperiment - Class in net.sourceforge.seqware.common.model
ShareExperiment generated by hbm2java
ShareExperiment() - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
 
ShareExperiment(int, Experiment, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
 
ShareExperiment(int, Experiment, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
 
ShareExperimentDAO - Interface in net.sourceforge.seqware.common.dao
 
ShareExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ShareExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
ShareExperimentService - Interface in net.sourceforge.seqware.common.business
 
ShareExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ShareExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
ShareFile - Class in net.sourceforge.seqware.common.model
ShareFile generated by hbm2java
ShareFile() - Constructor for class net.sourceforge.seqware.common.model.ShareFile
 
ShareFile(int, File, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile
 
ShareFile(int, File, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile
 
ShareFileDAO - Interface in net.sourceforge.seqware.common.dao
 
ShareFileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ShareFileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
ShareFileService - Interface in net.sourceforge.seqware.common.business
 
ShareFileServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ShareFileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
ShareLane - Class in net.sourceforge.seqware.common.model
ShareLane generated by hbm2java
ShareLane() - Constructor for class net.sourceforge.seqware.common.model.ShareLane
 
ShareLane(int, Lane, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane
 
ShareLane(int, Lane, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane
 
ShareLaneDAO - Interface in net.sourceforge.seqware.common.dao
 
ShareLaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ShareLaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
ShareLaneService - Interface in net.sourceforge.seqware.common.business
 
ShareLaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ShareLaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
ShareProcessing - Class in net.sourceforge.seqware.common.model
ShareProcessing generated by hbm2java
ShareProcessing() - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
 
ShareProcessing(int, Processing, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
 
ShareProcessing(int, Processing, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
 
ShareProcessingDAO - Interface in net.sourceforge.seqware.common.dao
 
ShareProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ShareProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
ShareProcessingService - Interface in net.sourceforge.seqware.common.business
 
ShareProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ShareProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
ShareSample - Class in net.sourceforge.seqware.common.model
ShareSample generated by hbm2java
ShareSample() - Constructor for class net.sourceforge.seqware.common.model.ShareSample
 
ShareSample(int, Sample, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample
 
ShareSample(int, Sample, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample
 
ShareSampleDAO - Interface in net.sourceforge.seqware.common.dao
 
ShareSampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ShareSampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
ShareSampleService - Interface in net.sourceforge.seqware.common.business
 
ShareSampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ShareSampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
ShareStudy - Class in net.sourceforge.seqware.common.model
 
ShareStudy() - Constructor for class net.sourceforge.seqware.common.model.ShareStudy
 
ShareStudyDAO - Interface in net.sourceforge.seqware.common.dao
 
ShareStudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ShareStudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
 
ShareStudyService - Interface in net.sourceforge.seqware.common.business
 
ShareStudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ShareStudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
 
ShareValidatorController - Class in net.sourceforge.solexatools.webapp.controller
 
ShareValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
 
ShareWorkflowRun - Class in net.sourceforge.seqware.common.model
 
ShareWorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
ShareWorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao
 
ShareWorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
ShareWorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
 
ShareWorkflowRunService - Interface in net.sourceforge.seqware.common.business
 
ShareWorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ShareWorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
 
SignUpController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
SignUpController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SignUpController
 
SimpleFileLock - Class in net.sourceforge.seqware.common.util.filetools.lock
Deprecated.  
SimpleFileLock(String) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated.  
SimpleFileLock(File) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated.  
SimpleModelManager - Class in com.github.seqware.queryengine.impl
A Simple implementation of the CreateUpdateManager interface.
SimpleModelManager() - Constructor for class com.github.seqware.queryengine.impl.SimpleModelManager
 
SimpleModelManager.AtomStatePair - Class in com.github.seqware.queryengine.impl
 
SimpleModelManager.AtomStatePair(Atom, CreateUpdateManager.State) - Constructor for class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
SimplePersistentBackEnd - Class in com.github.seqware.queryengine.impl
A toy backend implementation that writes all stores objects to disk using Java persistence.
SimplePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
single - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
 
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
SIZE_COUNT_FILE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil
 
SIZE_COUNT_TREE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil
 
sleep(int) - Static method in class net.sourceforge.seqware.common.util.processtools.ProcessTools
 
SNV - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SNVMix - Class in net.sourceforge.seqware.pipeline.modules
Syntax: ./SNVMix2 -m [-i ] [-o ] [-T | -C | -F] [-p < q | m | s >] [-t < mb | m | b | M | Mb | MB | SNVMix1>] [-q <#>] [-Q <#>] [-a/-b/-d <#,#,#>] [-M ] [-h] Required: -m model file, a line for mu and a line for pi, three space-separated values each, like: mu 0.xxxxxxxx 0.xxxxxxxx 0.xxxxxxxx pi 0.xxxxxxxx 0.xxxxxxxx 0.xxxxxxxx Optional: -i quality pileup, from pileup2matlab.pl script (def: STDIN) -o where to put the results (def: STDOUT) -T | -C | -F Train, Classify or Filter (def: Classify) -p q|m|s Input pileup format (def: s) q = quality m = MAQ s = SAMtools -t mb|m|b|M|Mb|MB|SNVMix1 Filter type (def: mb) mb Lowest between map and base quality m Filter on map, and use as surrogate for base quality b Filter on base quality, take map quality as 1 M Filter on map quality but use only base quality Mb Filter on map quality and use both map and base qualities MB Filter on map quality AND base quality SNVMix1 Filter on base quality and map quality, afterwards consider them perfect -q # Cutoff Phred value for Base Quality, anything <= this value is ignored (def: Q19) -Q # Cutoff Phred value for Map Quality, anything <= this value is ignored (def: Q19) Training parameters: -a #,#,# Provide alpha training parameters -b #,#,# Provide beta training parameters -d #,#,# Provide delta training parameters -M Provide a file containing training parameters (will override -a, -b and -d) Values are space-separated: alpha # # # beta # # # delta # # # -apply-filter -perl-path Path to perl installation -filter-path Path to the filter script -threshold THRESHOLD is given, then SNVs will be reported when the selected probability exceeds this -c [2|3] TYPE is the number of classes to consider '2' considers only AA and {AB U BB} (default) '3' considers AA, AB and BB -h this message
SNVMix() - Constructor for class net.sourceforge.seqware.pipeline.modules.SNVMix
 
SOFeatureImporter - Class in com.github.seqware.queryengine.system.importers
Importer using a new interface to the parameters in order to support SO importing and the specification of a tag set and reference to attach to.
SOFeatureImporter() - Constructor for class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
someString() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource
 
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
source - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
 
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
 
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
 
SOURCE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
sourceSet - Variable in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper
the feature set that we will be reading
SpliceJunctionCounts - Class in net.sourceforge.seqware.pipeline.modules.quantification
Calculate counts per junction given a BAM file of aligned reads and a list of splice junctions.
SpliceJunctionCounts() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
 
splitFile(File, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
spotdecodemethod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
 
spotdecodespec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
 
spotdescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
SQLQUERYFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
SRF2Fastq - Class in net.sourceforge.seqware.pipeline.modules.io
 
SRF2Fastq() - Constructor for class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
 
srf2fastq - Class in net.sourceforge.seqware.pipeline.modules
 
srf2fastq() - Constructor for class net.sourceforge.seqware.pipeline.modules.srf2fastq
 
SRF2Fastq_0_7_2 - Class in net.sourceforge.seqware.pipeline.modules.io
 
SRF2Fastq_0_7_2() - Constructor for class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
 
stackTraceToString(Throwable) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
 
START_ALL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
START_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
START_PMC_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
START_PMCSI_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
START_QUAL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
startCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
 
startCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
 
startCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
 
startCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
An alternate runner that launches a process and returns it so that the caller can process it's output directly.
STARTCOUNTDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
STARTDUMP_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
startPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
startPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
startTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
 
startTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
 
status - Variable in exception net.sourceforge.seqware.common.util.ExitException
 
statusCounts - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
stderr(String) - Static method in class com.github.seqware.queryengine.common.Log
 
stderr - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
stderr(String) - Static method in class net.sourceforge.seqware.common.util.Log
 
StdErr - Class in net.sourceforge.seqware.common.util.processtools.stderr
 
StdErr() - Constructor for class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
 
stderr2string(Process) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
 
StderrRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module
Annotation type to tag where to start Stderr redirect Created by IntelliJ IDEA.
stdout(String) - Static method in class com.github.seqware.queryengine.common.Log
 
stdout - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
stdout(String) - Static method in class net.sourceforge.seqware.common.util.Log
 
StdOut - Class in net.sourceforge.seqware.common.util.processtools.stdout
 
StdOut() - Constructor for class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
stdout2file(Process, File, boolean) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
stdout2file(Process, ArrayList<File>, boolean, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
stdout2fileBinary(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
stdout2fileBinary(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
stdout2fileEncoded(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
stdout2fileEncoded(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
stdout2fileEncodedStripQualPrimer(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
STDOUTERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
StdoutRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module
Interface for declaring when to do the Created by IntelliJ IDEA.
stop() - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain
 
STOP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
stopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
stopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
storage - Variable in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
StorageInterface - Class in com.github.seqware.queryengine.impl
Defines a very basic interface that allows us to abstract whether we write to files or to databases or just keep things in memory
StorageInterface() - Constructor for class com.github.seqware.queryengine.impl.StorageInterface
 
store(Atom...) - Method in interface com.github.seqware.queryengine.impl.BackEndInterface
Store obj in the back-end.
store(Atom...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
Store - Class in net.sourceforge.seqware.queryengine.backend.store
 
Store() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.Store
 
StoreInterface - Interface in net.sourceforge.seqware.queryengine.backend.store
 
strand - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
strand - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
STRAND_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
STRINGID - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
StringId - Class in net.sourceforge.seqware.queryengine.backend.model
 
StringId() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.StringId
 
StringIdTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
StringIdTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
 
StringUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus
 
StringUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.StringUtils
 
Study - Class in net.sourceforge.seqware.common.model
 
Study() - Constructor for class net.sourceforge.seqware.common.model.Study
 
study - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudySet
 
STUDY_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
STUDY_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
 
STUDY_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
STUDY_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
STUDY_TITLE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
STUDY_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
 
studyabstract - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyAttribute - Class in net.sourceforge.seqware.common.model
StudyAttribute generated by hbm2java
StudyAttribute() - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
 
StudyAttribute(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
 
StudyAttribute(int, Study, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
 
studyattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES
 
StudyAttributeDAO - Interface in net.sourceforge.seqware.common.dao
 
StudyAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
StudyAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
 
studyattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
StudyBuildTree - Class in net.sourceforge.solexatools.util
 
StudyBuildTree() - Constructor for class net.sourceforge.solexatools.util.StudyBuildTree
 
StudyController - Class in net.sourceforge.solexatools.webapp.controller
StudyController
StudyController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController
 
StudyController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController
 
StudyDAO - Interface in net.sourceforge.seqware.common.dao
 
StudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
StudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
studydescription - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyHtmlUtil - Class in net.sourceforge.solexatools.util
 
StudyHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.StudyHtmlUtil
 
StudyIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
StudyIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource
 
StudyIdFilesTSVResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
StudyIdFilesTSVResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource
 
StudyIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
 
StudyIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter
 
StudyIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
StudyIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
 
StudyLink - Class in net.sourceforge.seqware.common.model
StudyLink generated by hbm2java
StudyLink() - Constructor for class net.sourceforge.seqware.common.model.StudyLink
 
StudyLink(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink
 
StudyLink(int, Study, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink
 
studylink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS
 
StudyLinkDAO - Interface in net.sourceforge.seqware.common.dao
 
StudyLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
StudyLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
 
studylinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
StudyList - Class in net.sourceforge.seqware.common.model.lists
 
StudyList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyList
 
StudyListController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
StudyListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListController
 
StudyListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
 
StudyListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
 
StudyListDetailsFlatController - Class in net.sourceforge.solexatools.webapp.controller
 
StudyListDetailsFlatController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
studyref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
studyref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
StudyReportBoxController - Class in net.sourceforge.solexatools.webapp.controller
 
StudyReportBoxController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
StudyReportController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
StudyReportController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportController
 
StudyReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
StudyReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
 
StudyReportTableController - Class in net.sourceforge.solexatools.webapp.controller
 
StudyReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
StudyResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
StudyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyResource
 
StudySampleReportFileLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
 
StudySampleReportFileLineItem(Sample, Sample, IUS, File) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
 
StudySampleReportLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
 
StudySampleReportLineItem(Sample, Sample, String[]) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
 
StudyService - Interface in net.sourceforge.seqware.common.business
 
StudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
StudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
StudySet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudySet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudySet
 
StudySetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
StudySetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudySetupController
 
studytitle - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyType - Class in net.sourceforge.seqware.common.model
 
StudyType() - Constructor for class net.sourceforge.seqware.common.model.StudyType
 
StudyType - Class in net.sourceforge.seqware.queryengine.webservice.model
A Study is a container for a sequencing investigation that may comprise multiple experiments.
StudyType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
studytype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyType.DESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.DESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyType.DESCRIPTOR.STUDYTYPE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.DESCRIPTOR.STUDYTYPE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
 
StudyType.STUDYATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES
 
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
 
StudyType.STUDYLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS
 
StudyType.STUDYLINKS.STUDYLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
 
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
 
StudyType.STUDYLINKS.STUDYLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
 
StudyTypeDAO - Interface in net.sourceforge.seqware.common.dao
 
StudyTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
StudyTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
 
StudyTypeService - Interface in net.sourceforge.seqware.common.business
 
StudyTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
StudyTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
 
StudyUpdateValidator - Class in net.sourceforge.solexatools.validation
 
StudyUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyUpdateValidator
 
StudyValidator - Class in net.sourceforge.solexatools.validation
 
StudyValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyValidator
 
subList(int, int, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
 
subList(HttpServletRequest, String, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
 
subList(HttpServletRequest, String, int, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
 
subListSD(HttpServletRequest, String, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
 
submission - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet
 
submissionComment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
submissionDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
submissionId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
SubmissionSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet
 
SubmissionType - Class in net.sourceforge.seqware.queryengine.webservice.model
A Submission type is used to describe an object that contains submission information, contacts for the submission, actions to be performed by the Archive, and file manifest.
SubmissionType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
SubmissionType.ACTIONS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS
 
SubmissionType.ACTIONS.ACTION - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
SubmissionType.ACTIONS.ACTION.ADD - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.ADD() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
 
SubmissionType.ACTIONS.ACTION.HOLD - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.HOLD() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
SubmissionType.ACTIONS.ACTION.MODIFY - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.MODIFY() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
 
SubmissionType.ACTIONS.ACTION.RELEASE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.RELEASE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
 
SubmissionType.ACTIONS.ACTION.SUPPRESS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.SUPPRESS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
 
SubmissionType.ACTIONS.ACTION.VALIDATE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.VALIDATE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
 
SubmissionType.CONTACTS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.CONTACTS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS
 
SubmissionType.CONTACTS.CONTACT - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.CONTACTS.CONTACT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
 
SubmissionType.FILES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.FILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES
 
SubmissionType.FILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.FILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
 
SUBMITTED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
 
SUCCESS - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
 
SUCCESS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
 
SUCCESS - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
SUCCESS - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
sum - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
SummaryData - Class in net.sourceforge.solexatools.util
 
SummaryData() - Constructor for class net.sourceforge.solexatools.util.SummaryData
 
SummaryLaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller
 
SummaryLaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
 
SummaryLaunchWorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
 
SummaryLine - Class in net.sourceforge.solexatools.util
 
SummaryLine() - Constructor for class net.sourceforge.solexatools.util.SummaryLine
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.LaneValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.LoginValidator
Returns true if this Validator supports the specified Class, and false otherwise.
supports(Class) - Method in class net.sourceforge.solexatools.validation.SampleValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.StudyValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator
 
supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator
 
suppress - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
SV - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_COMPLEX - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_DELETION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_DELETION_AND_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_DISPERSED_DUPLICATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_DUPLICATION_AND_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_LOCATION_DOWNSTREAM - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_LOCATION_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_LOCATION_UPSTREAM - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_TANDEM_DUPLICATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
SV_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
svType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
sw - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
SwBadFileException - Exception in net.sourceforge.seqware.common.err
Created by IntelliJ IDEA.
SwBadFileException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
 
SwBadFileException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
 
SwBadFileException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
 
SwBadFileException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
 
SwBadModuleException - Exception in net.sourceforge.seqware.common.err
User: Xiaoshu Wang (xiao@renci.org) Date: 9/1/11 Time: 2:56 PM
SwBadModuleException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
 
SwBadModuleException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
 
SwBadModuleException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
 
SwBadModuleException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
 
SwParameterException - Exception in net.sourceforge.seqware.common.err
Created by IntelliJ IDEA.
SwParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
 
SwParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
 
SwParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
 
SwParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
 
SWQEFactory - Class in com.github.seqware.queryengine.factory
This is the SeqWare Query Engine factory and should be used as the primary entry-point for developers.
SWQEFactory() - Constructor for class com.github.seqware.queryengine.factory.SWQEFactory
 
SWQEFactory.Model_Type - Enum in com.github.seqware.queryengine.factory
' These types describe different types of our model objects, for example the in memory objects load everything into memory.
SWQEFactory.Serialization_Type - Enum in com.github.seqware.queryengine.factory
These describe different types of serialization only
SWQEFactory.Storage_Type - Enum in com.github.seqware.queryengine.factory
These describe different types of our back-end, whether we store to files, to a database, or simply keep things in memory
SwRunnerParameterException - Exception in net.sourceforge.seqware.common.err
User: Xiaoshu Wang (xiao@renci.org) Date: 9/6/11 Time: 3:20 PM
SwRunnerParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
 
SwRunnerParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
 
SwRunnerParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
 
SwRunnerParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
 
SymLinkFileReporter - Class in net.sourceforge.seqware.pipeline.plugins
 
SymLinkFileReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
 

T

table - Variable in class net.sourceforge.seqware.webservice.resources.tables.DatabaseResource
 
TABLE_MODEL - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
TABLE_MODEL - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
TABLE_SEL - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
TABLE_SEL - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
 
Tag - Class in com.github.seqware.queryengine.model
A Tag an instance of a TagSpec which contains all three of the values necessary for a GVF (ex: ID=ID_1 or Variant_seq=A,G or Reference_seq=G ).
TAG - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
Tag - Class in net.sourceforge.seqware.queryengine.backend.model
 
Tag() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Tag
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
 
Tag.Builder - Class in com.github.seqware.queryengine.model
 
Tag.Builder() - Constructor for class com.github.seqware.queryengine.model.Tag.Builder
 
Tag.ValueType - Enum in com.github.seqware.queryengine.model
 
TAG_CHAR - Static variable in class com.github.seqware.queryengine.system.importers.OBOImporter
 
TagAnnotationByPositionImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
 
TagAnnotationByPositionImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationByPositionImporter
 
TagAnnotationImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
 
TagAnnotationImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationImporter
 
TagComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
 
TagComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.TagComparator
 
TagDumper - Class in net.sourceforge.seqware.queryengine.tools.exporters
 
TagDumper() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.TagDumper
 
Taggable<T> - Interface in com.github.seqware.queryengine.model.interfaces
Interface for all classes that can be tagged.
Taggable.NestedLevel - Class in com.github.seqware.queryengine.model.interfaces
This class represents both the tags that may be present at a particular level of the nested hash structure as well as tags that may be further up
Taggable.NestedLevel() - Constructor for class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
tagIndexTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
TagIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
TagIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagIO
 
TagKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
 
TagKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyCreator
 
TagKeyOnlyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
 
TagKeyOnlyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyOnlyCreator
 
TagResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
TagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.TagResource
 
tags - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
tags - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TAGS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
TAGS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
TagSet - Interface in com.github.seqware.queryengine.model
A set of Tag specifications
TagSet.Builder - Class in com.github.seqware.queryengine.model
 
TagSet.Builder() - Constructor for class com.github.seqware.queryengine.model.TagSet.Builder
 
TAGSET_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
TagSetCreator - Class in com.github.seqware.queryengine.system
Quick and dirty TagSet creator.
TagSetCreator() - Constructor for class com.github.seqware.queryengine.system.TagSetCreator
 
tagSetIDs - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
TagSetIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
TagSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
 
TAGSETS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
TAGSPECIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
TagSpecIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
TagSpecIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
 
TagTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
TagTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
 
TagUtils - Class in net.sourceforge.solexatools.util
 
TagUtils() - Constructor for class net.sourceforge.solexatools.util.TagUtils
 
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
 
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
 
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
 
taxonid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
 
temp - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
templateFile - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
TemplateResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
TemplateResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.TemplateResource
 
test() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
 
test() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
test() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
test(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest
 
TEST_FAMILY_INBYTES - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage
 
TEST_QUALIFIER_INBYTES - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage
 
TEST_TABLE_PREFIX - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage
 
testBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
testBundle(File, File, String, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
A bundle test occurs without metadata writeback
TestDatabaseCreator - Class in net.sourceforge.seqware.metadb.util
 
TestDatabaseCreator() - Constructor for class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
 
testIfNull(Object) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
 
testIfNull(Object) - Method in class net.sourceforge.seqware.webservice.resources.BasicResource
 
testIfNull(Object) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
TestModule - Class in net.sourceforge.seqware.pipeline.module
This is an empty module mainly for testing purpose.
TestModule() - Constructor for class net.sourceforge.seqware.pipeline.module.TestModule
 
TextDumper - Class in net.sourceforge.seqware.queryengine.tools.exporters
 
TextDumper() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.TextDumper
 
thickEnd - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
thickStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
TIMESTAMP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.ExperimentList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.FileList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.IUSList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.LaneList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.ProcessingList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.ReturnValueList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.SampleList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.SequencerRunList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.StudyList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
 
TmpFileStorage - Class in com.github.seqware.queryengine.impl
Stores objects in the temporary directory of the disk
TmpFileStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.TmpFileStorage
 
toBaseN(int, int) - Static method in class com.github.seqware.queryengine.kernel.Compression
Converts an integer into a string representation of certain base.
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
toBuilder() - Method in class com.github.seqware.queryengine.model.Analysis
 
toBuilder() - Method in interface com.github.seqware.queryengine.model.AnalysisSet
Create a AnalysisSet builder started with a copy of this
toBuilder() - Method in class com.github.seqware.queryengine.model.Feature
 
toBuilder() - Method in class com.github.seqware.queryengine.model.FeatureSet
Create an FeatureSet builder started with a copy of this
toBuilder() - Method in interface com.github.seqware.queryengine.model.Group
Create a Group builder started with a copy of this
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
 
toBuilder() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Create an ACL builder started with a copy of this
toBuilder() - Method in interface com.github.seqware.queryengine.model.interfaces.Buildable
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.Reference
Create an ACL builder started with a copy of this
toBuilder() - Method in interface com.github.seqware.queryengine.model.ReferenceSet
Create a ReferenceSet builder started with a copy of this
toBuilder() - Method in class com.github.seqware.queryengine.model.Tag
Create an ACL builder started with a copy of this
toBuilder() - Method in interface com.github.seqware.queryengine.model.TagSet
Create an FeatureSet builder started with a copy of this
toBuilder() - Method in class com.github.seqware.queryengine.model.User
Create an User builder started with a copy of this
TOMBSTONE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
toString() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
toString() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
 
toString() - Method in class com.github.seqware.queryengine.util.FSGID
 
toString() - Method in class com.github.seqware.queryengine.util.SGID
 
toString() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
toString() - Method in class net.sourceforge.seqware.common.model.Expense
 
toString() - Method in class net.sourceforge.seqware.common.model.Experiment
 
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
 
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
 
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
 
toString() - Method in class net.sourceforge.seqware.common.model.File
 
toString() - Method in class net.sourceforge.seqware.common.model.FileType
 
toString() - Method in class net.sourceforge.seqware.common.model.Invoice
 
toString() - Method in class net.sourceforge.seqware.common.model.IUS
 
toString() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
 
toString() - Method in class net.sourceforge.seqware.common.model.Lane
 
toString() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
 
toString() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
toString() - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
toString() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
toString() - Method in class net.sourceforge.seqware.common.model.Organism
 
toString() - Method in class net.sourceforge.seqware.common.model.Platform
 
toString() - Method in class net.sourceforge.seqware.common.model.Processing
 
toString() - Method in class net.sourceforge.seqware.common.model.Project
 
toString() - Method in class net.sourceforge.seqware.common.model.Registration
 
toString() - Method in class net.sourceforge.seqware.common.model.Sample
 
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRun
 
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
 
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
 
toString() - Method in class net.sourceforge.seqware.common.model.ShareStudy
 
toString() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
 
toString() - Method in class net.sourceforge.seqware.common.model.Study
 
toString() - Method in class net.sourceforge.seqware.common.model.StudyType
 
toString() - Method in class net.sourceforge.seqware.common.model.Workflow
 
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
 
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
 
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
 
toString() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
toString() - Method in class net.sourceforge.seqware.common.module.ReturnValue
 
toString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusJob
 
toString(WorkflowRunReportRow, StringBuilder) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
 
totalDataBlocks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
totalReads - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
totalSpots - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
totalSteps - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
totalSteps - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
trace(Object) - Static method in class com.github.seqware.queryengine.common.Log
See Category.debug(Object).
trace(Object, Throwable) - Static method in class com.github.seqware.queryengine.common.Log
See Category.debug(Object,Throwable).
trace(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.debug(Object).
trace(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.debug(Object,Throwable).
transcriptassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
transcriptId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
transcriptsequencing - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
translatedSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
TRANSLOCATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TRANSLOCATION_COMPLEX - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TRANSLOCATION_INTERCHR - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TRANSLOCATION_INTRACHR - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TRANSLOCATION_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
translocationDestinationContig - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
translocationDestinationStartPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
translocationDestinationStopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
translocationType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TreeNodeHtmlUtil - Class in net.sourceforge.solexatools.util
 
TreeNodeHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
TrimAdapter - Class in net.sourceforge.seqware.pipeline.modules.alignment
Trim adapter segment (and any following sequence) from reads.
TrimAdapter() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
 
TrimAllReads - Class in net.sourceforge.seqware.pipeline.modules.alignment
Trim all reads down to a user-defined length.
TrimAllReads() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
 
TrimCountAdapter - Class in net.sourceforge.seqware.pipeline.modules.alignment
Trim adapter segment (and any following sequence) from reads, and get count & % of reads that contain adapter segment.
TrimCountAdapter() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
 
TTLable - Interface in com.github.seqware.queryengine.model.interfaces
Interface for object that can be set to expire at some point in the future.
type - Variable in class com.github.seqware.queryengine.util.LazyReference
 
type - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TYPE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
TYPE_TREE - Static variable in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
TYPE_TREE - Static variable in class net.sourceforge.solexatools.util.StudyHtmlUtil
 
TYPE_TREE_COMPLETED - Static variable in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
 
TYPE_TREE_RUNNNING - Static variable in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
 

U

U87LargeDeletionVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
U87LargeDeletionVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.U87LargeDeletionVariantImportWorker
 
U87TranslocationVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
U87TranslocationVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.U87TranslocationVariantImportWorker
 
unBindSessionFromTheThread() - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
 
UNCKerberos - Class in net.sourceforge.solexatools.authentication
 
UNCKerberos() - Constructor for class net.sourceforge.solexatools.authentication.UNCKerberos
 
UNCKerberos.NamePasswordCallbackHandler - Class in net.sourceforge.solexatools.authentication
 
UNCKerberos.NamePasswordCallbackHandler(String, String) - Constructor for class net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler
 
Unclassified - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
 
uniqRead - Class in net.sourceforge.seqware.pipeline.modules.qc
Performing per lane based statistics Underlying script: sw_module_readDepth.pl Necessary programs: perl Expected output: read_depth.txt
uniqRead() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
 
UNKNOWN - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
 
UNKNOWN_TYPE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
UNKNOWN_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
UNKNOWN_ZYGOSITY - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
unmarshal(FileList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
 
unmarshal(IUSList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
 
unmarshal(LaneList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
 
unmarshal(String) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeXML
 
unMarshal(T, Reader) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject
Turn an XML stream into an object, if possible.
unMarshal(Document, T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject
Turn an XML stream into an object, if possible.
unMarshal(JaxbObject, Object, String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
 
unpackageBundle(File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
unpackageBundleFromS3(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
unpackArchive(File, File, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil
Unpack a zip file
UNPROCESSED_ATTRIBUTES - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Unprocessed attributes, many of these could be parsed further, but this would take work to account for multi-individual files and the like
UnZip - Class in net.sourceforge.seqware.pipeline.tools
 
UnZip() - Constructor for class net.sourceforge.seqware.pipeline.tools.UnZip
 
unzipFile(File, File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
FIXME: should make this optional to keep the original file
unzipFileOld(File, File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
FIXME: should make this optional to keep the original file
unzipPkg(String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner
FIXME: this needs to be migrated to something that is ZIP64 aware.
update(Atom...) - Method in interface com.github.seqware.queryengine.impl.BackEndInterface
Crawl through obj and update changes in the back-end.
update(Atom...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
update(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
 
update(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
update(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
update(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
 
update(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
 
update(Integer, FileAttribute) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
 
update(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService
 
update(File) - Method in interface net.sourceforge.seqware.common.business.FileService
 
update(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
Updates an instance of ExperimentLibraryDesign in the database.
update(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
Updates an instance of Experiment in the database.
update(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
update(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
Updates an instance of ExperimentSpotDesignReadSpec in the database.
update(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
Updates an instance of ExperimentSpotDesign in the database.
update(Integer, FileAttribute) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
 
update(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
Updates an instance of File in the database.
update(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
update(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
update(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
update(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
update(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
update(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Updates an instance of Lane in the database.
update(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
update(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
update(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
update(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
update(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
update(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
update(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
update(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
Updates an instance of Processing in the database.
update(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
update(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
update(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
Updates an instance of Project in the database.
update(RegistrationDTO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
 
update(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Updates an instance of Sample in the database.
update(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
update(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Updates an instance of SequencerRun in the database.
update(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
update(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
update(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
update(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
update(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
update(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
update(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
Updates an instance of ShareStudy in the database.
update(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
Updates an instance of ShareWorkflowRun in the database.
update(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Updates an instance of Study in the database.
update(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
update(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
Updates an instance of StudyType in the database.
update(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
update(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
update(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
update(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
update(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
update(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
update(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
update(WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
update(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
update(Registration, WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
update(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
update(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
update(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
update(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
update(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
update(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
update(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
update(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
update(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
 
update(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
 
update(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
 
update(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
 
update(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
 
update(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
 
update(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
update(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
update(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
 
update(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
update(RegistrationDTO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
 
update(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
update(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
update(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
update(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
update(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
update(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
update(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
update(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
update(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
update(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
update(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
update(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
update(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
update(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
 
update(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
update(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
update(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
update(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
update(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
update(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
update(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
update(WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
update(Registration, WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
update(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
update(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
update(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
update(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
 
update(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
update(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
update(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
 
update(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
 
update(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
 
update(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
 
update(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
 
update(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
update(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
update(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
 
update(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
update(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
update(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
 
update(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
 
update(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
 
update(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
 
update(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
 
update(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
Updates an instance of File in the database.
update(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
update(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
update(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
update(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
 
update(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
Updates an instance of Lane in the database.
update(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
update(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO
 
update(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
 
update(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
 
update(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
 
update(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
Updates an instance of Lane in the database.
update(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
update(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
 
update(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
 
update(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
 
update(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
Updates an instance of Processing in the database.
update(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
update(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
 
update(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
 
update(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
 
update(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
update(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
 
update(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
 
update(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
 
update(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
 
update(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
Updates an instance of Registration in the database.
update(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
 
update(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
Updates an instance of Sample in the database.
update(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
update(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
 
update(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
update(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
update(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
update(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
update(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
update(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
update(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
update(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
Updates an instance of ShareStudy in the database.
update(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
Updates an instance of ShareWorkflowRun in the database.
update(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
 
update(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
update(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
update(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
 
update(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
 
update(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
 
update(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
update(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
update(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
update(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
update(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
update(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
update(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
 
update(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
update(WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
update(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
update(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
update(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
update(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
update(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
update(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
 
update(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
update(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
update(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
update(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
update(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
 
update(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
update(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
update(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
 
update(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
 
update(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
 
update(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
 
update(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
 
update(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
 
update(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
 
update(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
 
update(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
 
update(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
 
update(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
update(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
update(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
 
update(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
update(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
update(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
 
update(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
 
update(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
 
update(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
 
update(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
 
update(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
 
update(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
update(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
 
update(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
update(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
update(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
 
update(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
 
update(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
 
update(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
update(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
update(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
 
update(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
 
update(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
 
update(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
 
update(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
 
update(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
update(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
update(WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
update(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
update(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
update_processing_event(int, ReturnValue) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
update_processing_status(int, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
update_processing_workflow_run(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
updateACL(ACL) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateAnalysisPlugin(AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateAnalysisSet(AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateAttribute(AttributeDto) - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
 
updateAttribute(AttributeDto) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
 
updateDetached(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
 
updateDetached(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
updateDetached(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
 
updateDetached(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
 
updateDetached(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
 
updateDetached(File) - Method in interface net.sourceforge.seqware.common.business.FileService
 
updateDetached(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService
 
updateDetached(FileType) - Method in interface net.sourceforge.seqware.common.business.FileTypeService
 
updateDetached(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
 
updateDetached(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
updateDetached(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
 
updateDetached(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
 
updateDetached(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
 
updateDetached(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
updateDetached(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
 
updateDetached(FileType) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
 
updateDetached(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
updateDetached(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
 
updateDetached(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
updateDetached(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
 
updateDetached(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
updateDetached(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
updateDetached(LibrarySelection) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
 
updateDetached(LibrarySource) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
 
updateDetached(LibraryStrategy) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
 
updateDetached(Organism) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
 
updateDetached(Platform) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
 
updateDetached(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
updateDetached(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
updateDetached(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
updateDetached(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
updateDetached(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
updateDetached(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
updateDetached(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
updateDetached(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
 
updateDetached(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
updateDetached(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
 
updateDetached(Registration) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
 
updateDetached(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
updateDetached(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
updateDetached(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
updateDetached(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
 
updateDetached(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
updateDetached(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
updateDetached(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
updateDetached(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
updateDetached(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
updateDetached(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
 
updateDetached(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
 
updateDetached(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
updateDetached(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
updateDetached(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
 
updateDetached(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
updateDetached(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
updateDetached(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
updateDetached(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
updateDetached(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
updateDetached(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
updateDetached(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
updateDetached(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
updateDetached(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
updateDetached(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
updateDetached(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
 
updateDetached(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
updateDetached(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
 
updateDetached(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
updateDetached(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
 
updateDetached(LibrarySelection) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
 
updateDetached(LibrarySource) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
 
updateDetached(LibraryStrategy) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
 
updateDetached(Organism) - Method in interface net.sourceforge.seqware.common.business.OrganismService
 
updateDetached(Platform) - Method in interface net.sourceforge.seqware.common.business.PlatformService
 
updateDetached(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
 
updateDetached(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
 
updateDetached(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
 
updateDetached(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
 
updateDetached(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
 
updateDetached(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
 
updateDetached(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
updateDetached(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
 
updateDetached(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
 
updateDetached(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService
 
updateDetached(Registration) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
 
updateDetached(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
updateDetached(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
updateDetached(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
updateDetached(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
 
updateDetached(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
 
updateDetached(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
 
updateDetached(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
 
updateDetached(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
 
updateDetached(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
 
updateDetached(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
 
updateDetached(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
 
updateDetached(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
updateDetached(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
updateDetached(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
 
updateDetached(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
updateDetached(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
 
updateDetached(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
updateDetached(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
 
updateDetached(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
updateDetached(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
 
updateDetached(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
 
updateDetached(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
updateDetached(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
 
updateDetached(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
updateDetached(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
 
updateDetached(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
 
updateDetached(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
 
updateDetached(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
 
updateDetached(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
updateDetached(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
 
updateDetached(FileType) - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO
 
updateDetached(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
updateDetached(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
 
updateDetached(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
 
updateDetached(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
 
updateDetached(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
 
updateDetached(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
updateDetached(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
 
updateDetached(FileType) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate
 
updateDetached(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
updateDetached(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
 
updateDetached(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
updateDetached(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
 
updateDetached(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
updateDetached(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
 
updateDetached(LibrarySelection) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
 
updateDetached(LibrarySource) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
 
updateDetached(LibraryStrategy) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
 
updateDetached(Organism) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
 
updateDetached(Platform) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
 
updateDetached(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
updateDetached(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
 
updateDetached(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
 
updateDetached(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
 
updateDetached(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
 
updateDetached(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
updateDetached(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
 
updateDetached(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
 
updateDetached(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
 
updateDetached(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
 
updateDetached(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
 
updateDetached(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
updateDetached(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
 
updateDetached(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
updateDetached(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
 
updateDetached(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
updateDetached(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
updateDetached(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
updateDetached(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
updateDetached(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
updateDetached(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
 
updateDetached(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
 
updateDetached(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
updateDetached(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
updateDetached(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
 
updateDetached(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
updateDetached(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
updateDetached(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
updateDetached(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
updateDetached(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
updateDetached(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
updateDetached(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
updateDetached(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
updateDetached(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
updateDetached(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
updateDetached(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
updateDetached(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
 
updateDetached(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
updateDetached(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
 
updateDetached(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
updateDetached(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
 
updateDetached(LibrarySelection) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO
 
updateDetached(LibrarySource) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO
 
updateDetached(LibraryStrategy) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO
 
updateDetached(Organism) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO
 
updateDetached(Platform) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO
 
updateDetached(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
updateDetached(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
 
updateDetached(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
 
updateDetached(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
 
updateDetached(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
 
updateDetached(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
 
updateDetached(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
 
updateDetached(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
 
updateDetached(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
 
updateDetached(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
 
updateDetached(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
 
updateDetached(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
updateDetached(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
 
updateDetached(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
updateDetached(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
 
updateDetached(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
 
updateDetached(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
 
updateDetached(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
 
updateDetached(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
 
updateDetached(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
 
updateDetached(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
 
updateDetached(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
 
updateDetached(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
updateDetached(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
updateDetached(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
 
updateDetached(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
updateDetached(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
 
updateDetached(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
 
updateDetached(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
 
updateDetached(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
 
updateDetached(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
 
updateDetached(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
updateDetached(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
 
updateDetached(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
updateDetached(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
 
updateFeature(Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateFeatureSet(FeatureSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateGroup(Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateLane(Sample, MultipartFile, MultipartFile, String, String, Registration) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
 
updateOwners(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
 
updateOwners(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
 
updateOwners(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
 
updateOwners(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
 
updateReference(Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateReferenceSet(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateSelectedIds(HttpServletRequest, String, boolean, List<String>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
 
updateTag(Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateTagSet(TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateUser(User) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
 
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
updateWorkflow(int, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
 
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
updateWorkflowRun(int, String, String, String, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
updateWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
 
upgradeFeatureSGID(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
 
uploadFile(Study, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
 
uploadFile(Experiment, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
 
uploadFile(Sample, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
 
uploadFile(Lane, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
 
uploadFile(IUS, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
 
uploadFile(Processing, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
 
uploadFile(SequencerRun, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
 
uploadFile(Study, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
uploadFile(Experiment, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
uploadFile(Sample, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
uploadFile(Lane, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
uploadFile(IUS, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
uploadFile(Processing, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
uploadFile(SequencerRun, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
 
UploadFile - Class in net.sourceforge.seqware.common.business
 
UploadFile() - Constructor for class net.sourceforge.seqware.common.business.UploadFile
 
UploadFileController - Class in net.sourceforge.solexatools.webapp.controller
 
UploadFileController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
UploadFileController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileController
 
UploadFileSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
UploadFileSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
 
UploadFileValidator - Class in net.sourceforge.solexatools.validation
 
UploadFileValidator() - Constructor for class net.sourceforge.solexatools.validation.UploadFileValidator
 
UploadSequence - Class in net.sourceforge.seqware.common.model
 
UploadSequence() - Constructor for class net.sourceforge.seqware.common.model.UploadSequence
 
UploadSequenceController - Class in net.sourceforge.solexatools.webapp.controller
 
UploadSequenceController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
UploadSequenceController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
 
UploadSequenceSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
UploadSequenceSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
 
UploadSequenceValidator - Class in net.sourceforge.solexatools.validation
 
UploadSequenceValidator() - Constructor for class net.sourceforge.solexatools.validation.UploadSequenceValidator
 
url - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
 
urlLabel - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
 
urlString - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
User - Class in com.github.seqware.queryengine.model
A user of the Generic Feature Store.
User.Builder - Class in com.github.seqware.queryengine.model
 
User.Builder() - Constructor for class com.github.seqware.queryengine.model.User.Builder
 
USER_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
UserIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
UserIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.UserIO
 
USERS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
UtilIO - Class in com.github.seqware.queryengine.impl.protobufIO
 
UtilIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.UtilIO
 
Utility - Class in com.github.seqware.queryengine.system
Utility procedures for interacting outside the API
Utility() - Constructor for class com.github.seqware.queryengine.system.Utility
 

V

Validate - Class in net.sourceforge.seqware.common.util.filetools.validate
 
Validate() - Constructor for class net.sourceforge.seqware.common.util.filetools.validate.Validate
 
validate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
validate() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource
 
validate() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource
 
validate(String) - Method in class net.sourceforge.solexatools.util.HTMLTagValidator
 
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.FileValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.LaneValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.LoginValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator
Validates the specified RegistrationDTO instance.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.StudyValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator
Validates the specified Object.
validateBundle(File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
validateEmail(String, String, Errors) - Method in class net.sourceforge.solexatools.validation.LoginValidator
Validates an email address.
validateEmailAddressesMatch(String, String, Errors) - Static method in class net.sourceforge.solexatools.validation.RegistrationValidator
Determines if the registration's email address and confirm email address match.
validateEmailNotInUse(String, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator
 
validateExists(MultipartFile, String, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
validateExpectedNumberReads(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
 
validateExpectedNumberReads(Sample, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator
 
validateExpectedNumberRuns(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
 
validateExpectedNumberRuns(Sample, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator
 
validateExtension(String, String, Integer, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
validateExtension(MultipartFile, MultipartFile, Integer, Errors) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
 
validateInvitationCode(String, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator
 
validateLaneCount(SequencerRunWizardDTO, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
 
validateName(String, Errors) - Method in class net.sourceforge.solexatools.validation.LaneValidator
Determines if the Lane's email address and confirm email address match.
validateName(String, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
Determines if the experiment's email address and confirm email address match.
validatePasswordsMatch(String, String, Errors) - Static method in class net.sourceforge.solexatools.validation.RegistrationValidator
Determines if the registration's password and confirm password match.
validateProtocol(String, String[], Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
 
validateRefLane(SequencerRun, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
 
validateTitle(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentUpdateValidator
 
validateTitle(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
Determines if the experiment's email address and confirm email address match.
validateTitle(String, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator
Determines if the sample's email address and confirm email address match.
validateTitle(Study, Errors) - Method in class net.sourceforge.solexatools.validation.StudyUpdateValidator
 
validateTitle(Study, Errors) - Method in class net.sourceforge.solexatools.validation.StudyValidator
Determines if the experiment's email address and confirm email address match.
ValidationReportService - Interface in net.sourceforge.seqware.common.business
A collection of reports useful when verifying that data in the SeqWare meta db is correct.
ValidationReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ValidationReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
 
ValidationReportServiceImpl.ReportEntry - Class in net.sourceforge.seqware.common.business.impl
 
ValidationReportServiceImpl.ReportEntry() - Constructor for class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
 
VALUE_SEPARATOR_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
valueOf(String) - Static method in enum com.github.seqware.queryengine.Constants.Term
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
Returns the enum constant of this type with the specified name.
valueOf(int) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
valueOf(Descriptors.EnumValueDescriptor) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.CreateUpdateManager.State
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Model_Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Serialization_Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Storage_Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.kernel.RPNStack.Operation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Feature.AdditionalAttributeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Feature.Strand
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.QueryInterface.Location
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Tag.ValueType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.module.ModuleMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflow.BasicWorkflow.Job
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.WorkflowExecutable
Returns the enum constant of this type with the specified name.
values() - Static method in enum com.github.seqware.queryengine.Constants.Term
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.CreateUpdateManager.State
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Model_Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Serialization_Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Storage_Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.kernel.RPNStack.Operation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Feature.AdditionalAttributeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Feature.Strand
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.QueryInterface.Location
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Tag.ValueType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.module.ModuleMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflow.BasicWorkflow.Job
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.WorkflowExecutable
Returns an array containing the constants of this enum type, in the order they are declared.
variableResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBaseBatchedPlugin
 
variableResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
This should be overridden with the result.
variableResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin
 
variableResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin
 
Variant - Class in net.sourceforge.seqware.queryengine.backend.model
 
Variant() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Variant
 
VariantConsequenceByPositionImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
 
VariantConsequenceByPositionImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceByPositionImporter
 
VariantConsequenceImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
 
VariantConsequenceImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceImporter
 
VariantImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
 
VariantImporter(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantImporter
 
VariantIteratorProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators
 
VariantIteratorProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.VariantIteratorProcessor
 
VariantProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
 
VariantProcessor(String, Store, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
VariantProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
 
VariantStatsProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
 
VariantStatsProcessor(String, BerkeleyDBStore, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor
 
VariantStatsProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor
 
VariantTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
VariantTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
 
VARIENT - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
VBYTES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VCF_CALLED_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_CONSENSUS_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_FILTER - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_HETEROZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_HOMOZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_INFO - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_READ_COUNTS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_REFERENCE_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_SECOND_ID - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCF_SNV - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
VCFDumper - Class in com.github.seqware.queryengine.system.exporters
This will dump VCF files given a FeatureSet that was originally imported from a VCF file.
VCFDumper(String[]) - Constructor for class com.github.seqware.queryengine.system.exporters.VCFDumper
 
VCFVariantImportWorker - Class in com.github.seqware.queryengine.system.importers.workers
Ported VCFVariantImportWorker now using our Hibernate-like entry.
VCFVariantImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
 
VCFVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
VCFVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.VCFVariantImportWorker
 
VDOUBLE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VenterGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
VenterGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.VenterGenomeVariantImportWorker
 
verify(String, char[]) - Method in class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
 
verifyFile(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
verifyInput() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
 
verifyInput() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
verifyInput() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
verifyOutput() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
 
verifyOutput() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
verifyOutput() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
verifyParameters() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface
 
verifyParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
 
verifyParameters() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
 
version - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
VERSION - Static variable in class net.sourceforge.seqware.pipeline.module.Module
 
version - Variable in class net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
Versionable<T extends Versionable> - Interface in com.github.seqware.queryengine.model.interfaces
Interface for versioning, versions are automatically generated and iterated when a new entity is derived from a parent entity.
VersionResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
VersionResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.VersionResource
 
VFLOAT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VINTEGER_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VLONG_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VSGIDREF_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VSTRING_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 

W

waitAndGetReturn(Process) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
Wait on a process to finish, then parse information into return value
warn(Object) - Static method in class com.github.seqware.queryengine.common.Log
See Category.warn(Object).
warn(Object, Throwable) - Static method in class com.github.seqware.queryengine.common.Log
See Category.warn(Object,Throwable).
warn(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.warn(Object).
warn(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.warn(Object,Throwable).
watchModuleRun(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect
 
watchModuleRun2(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.RedirectAspect
 
watchRunner(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect
 
watchWorkflow(String, String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
This method allows you to monitor a running Pegasus workflow using a statusCmd (typically something like "pegasus-status -l dir" and, if something goes wrong, it will return false.
watchWorkflow(String, String, int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
This method allows you to monitor a running Pegasus workflow using a statusCmd (typically something like "pegasus-status -l dir" and, if something goes wrong, it will return a ReturnValue with exit status of ReturnValue.FAILURE, ReturnValue.PROCESSING if still running, and ReturnValue.SUCCESS if finished OK.
WatsonGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
WatsonGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.WatsonGenomeVariantImportWorker
 
wfCount(Sample) - Static method in class net.sourceforge.solexatools.util.TagUtils
Returns count of the Sample related Workflow Runs.
WIGExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters
 
WIGExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.WIGExporter
 
WORKER_CHAR_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
workerName - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
Workflow - Class in net.sourceforge.seqware.common.model
 
Workflow() - Constructor for class net.sourceforge.seqware.common.model.Workflow
 
Workflow - Class in net.sourceforge.seqware.pipeline.workflow
FIXME: This Workflow object should have much of the implementation move to the common package, see WorkflowTools
Workflow(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflow.Workflow
 
Workflow - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
Workflow() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
Workflow(Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
WORKFLOW_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
WORKFLOW_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
WORKFLOW_RUN_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
 
WORKFLOW_RUN_STATUS - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
WORKFLOW_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
WORKFLOW_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
WORKFLOW_VERSION - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
WorkflowAttribute - Class in net.sourceforge.seqware.common.model
 
WorkflowAttribute() - Constructor for class net.sourceforge.seqware.common.model.WorkflowAttribute
 
WorkflowAttributeDAO - Interface in net.sourceforge.seqware.common.dao
 
WorkflowAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
 
WorkflowClassFinder - Class in net.sourceforge.seqware.pipeline.workflowV2
 
WorkflowClassFinder() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder
 
WorkflowContext - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus
 
WorkflowController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowController
 
WorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowController
 
WorkflowDAO - Interface in net.sourceforge.seqware.common.dao
 
WorkflowDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
 
WorkflowEngine - Interface in net.sourceforge.seqware.pipeline.workflowV2
 
WorkflowExecutable - Enum in net.sourceforge.seqware.pipeline.workflowV2.model
 
WorkflowExecutable - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus.object
 
WorkflowExecutable() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.WorkflowExecutable
 
WorkflowExecutableUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.pegasus
 
WorkflowExecutableUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.pegasus.WorkflowExecutableUtils
 
WorkflowIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
WorkflowIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
 
WorkflowInfo - Class in net.sourceforge.seqware.common.util.workflowtools
 
WorkflowInfo() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
WorkflowInterface - Interface in net.sourceforge.seqware.pipeline.workflowV2
 
WorkflowJobFactory - Class in net.sourceforge.seqware.pipeline.workflowV2
 
WorkflowJobFactory() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowJobFactory
 
WorkflowLauncher - Class in net.sourceforge.seqware.pipeline.plugins
 
WorkflowLauncher() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher
 
WorkflowLauncherV2 - Class in net.sourceforge.seqware.pipeline.plugins
 
WorkflowLauncherV2() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
 
WorkflowList - Class in net.sourceforge.seqware.common.model.lists
 
WorkflowList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowList
 
WorkflowListSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
WorkflowListSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
 
WorkflowManager - Class in net.sourceforge.seqware.common.util.workflowtools
 
WorkflowManager() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
 
WorkflowParam - Class in net.sourceforge.seqware.common.model
 
WorkflowParam() - Constructor for class net.sourceforge.seqware.common.model.WorkflowParam
 
WorkflowParamController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowParamController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
 
WorkflowParamController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
 
WorkflowParamDAO - Interface in net.sourceforge.seqware.common.dao
 
WorkflowParamDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowParamDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
 
WorkflowParamIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
WorkflowParamIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamIDResource
 
WorkflowParamList - Class in net.sourceforge.seqware.common.model.lists
 
WorkflowParamList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowParamList
 
WorkflowParamListController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowParamListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
 
WorkflowParamResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
WorkflowParamResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
 
WorkflowParamService - Interface in net.sourceforge.seqware.common.business
 
WorkflowParamServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
WorkflowParamServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
 
WorkflowParamSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowParamSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
 
WorkflowParamValidator - Class in net.sourceforge.solexatools.validation
 
WorkflowParamValidator() - Constructor for class net.sourceforge.solexatools.validation.WorkflowParamValidator
 
WorkflowParamValue - Class in net.sourceforge.seqware.common.model
 
WorkflowParamValue() - Constructor for class net.sourceforge.seqware.common.model.WorkflowParamValue
 
WorkflowParamValueController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowParamValueController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
 
WorkflowParamValueController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
 
WorkflowParamValueDAO - Interface in net.sourceforge.seqware.common.dao
 
WorkflowParamValueDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowParamValueDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
 
WorkflowParamValueIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
WorkflowParamValueIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueIDResource
 
WorkflowParamValueList - Class in net.sourceforge.seqware.common.model.lists
 
WorkflowParamValueList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
 
WorkflowParamValueResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
WorkflowParamValueResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
 
WorkflowParamValueService - Interface in net.sourceforge.seqware.common.business
 
WorkflowParamValueServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
WorkflowParamValueServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
 
WorkflowParamValueSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowParamValueSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
 
WorkflowReport - Class in net.sourceforge.seqware.common.hibernate
 
WorkflowReport() - Constructor for class net.sourceforge.seqware.common.hibernate.WorkflowReport
 
WorkflowReportResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
WorkflowReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource
 
WorkflowResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
WorkflowResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource
 
WorkflowResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
WorkflowResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
 
WorkflowRun - Class in net.sourceforge.seqware.common.model
 
WorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRun
 
WorkflowRunAttribute - Class in net.sourceforge.seqware.common.model
 
WorkflowRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
WorkflowRunAttributeDAO - Interface in net.sourceforge.seqware.common.dao
 
WorkflowRunAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowRunAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
 
WorkflowRunController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
 
WorkflowRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
 
WorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao
 
WorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
 
WorkflowRunHtmlUtil - Class in net.sourceforge.solexatools.util
 
WorkflowRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
 
WorkflowRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
WorkflowRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource
 
WorkflowRunIDProcessingsResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
WorkflowRunIDProcessingsResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource
 
WorkflowRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
WorkflowRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
 
WorkflowRunIDsFilter - Class in net.sourceforge.seqware.webservice.resources.filters
We presume there is either a runId or a testId, not both.
WorkflowRunIDsFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
 
WorkflowRunIDWorkflowResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
WorkflowRunIDWorkflowResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource
 
WorkflowRunList - Class in net.sourceforge.seqware.common.model.lists
 
WorkflowRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowRunList
 
WorkflowRunList2 - Class in net.sourceforge.seqware.common.model.lists
 
WorkflowRunList2() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
 
WorkflowRunParam - Class in net.sourceforge.seqware.common.model
 
WorkflowRunParam() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRunParam
 
WorkflowRunParamDAO - Interface in net.sourceforge.seqware.common.dao
 
WorkflowRunParamDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowRunParamDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
 
WorkflowRunParamService - Interface in net.sourceforge.seqware.common.business
 
WorkflowRunParamServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
WorkflowRunParamServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
 
WorkflowRunReport - Class in net.sourceforge.seqware.common.hibernate
Reports on workflow run metadata, returning either all workflow runs, all runs of a particular workflow, or a specific workflow run.
WorkflowRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
 
WorkflowRunReporter - Class in net.sourceforge.seqware.pipeline.plugins
 
WorkflowRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
 
WorkflowRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
WorkflowRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
 
WorkflowRunReportRow - Class in net.sourceforge.seqware.common.hibernate.reports
Contains the workflow's Processing events, the parent Processings, the input files, the output files, the identity and library samples, as well as the total running time.
WorkflowRunReportRow() - Constructor for class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
WorkflowRunResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
WorkflowRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
 
WorkflowRunService - Interface in net.sourceforge.seqware.common.business
 
WorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
WorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
 
WorkflowRunSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
 
WorkflowRunsFilter - Class in net.sourceforge.seqware.webservice.resources.filters
We presume there is either a runId or a testId, not both.
WorkflowRunsFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
 
WorkflowRunStatusResource - Class in net.sourceforge.seqware.queryengine.webservice.view
 
WorkflowRunStatusResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.WorkflowRunStatusResource
 
WorkflowRuntimeResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
WorkflowRuntimeResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource
 
WorkflowService - Interface in net.sourceforge.seqware.common.business
 
workflowService - Variable in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
 
WorkflowServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
WorkflowServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
 
WorkflowSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
WorkflowSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
 
WorkflowStatusChecker - Class in net.sourceforge.seqware.pipeline.plugins
This plugin lets you monitor the status of running workflows and updates the metadata object with their status.
WorkflowStatusChecker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
 
WorkflowTools - Class in net.sourceforge.seqware.common.util.workflowtools
This class provides methods for dealing with Pegasus workflow log directories for example watching a directory to detect when a workflow has failed or finished.
WorkflowTools() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
workflowTools - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
WorkflowValidator - Class in net.sourceforge.solexatools.validation
 
WorkflowValidator() - Constructor for class net.sourceforge.solexatools.validation.WorkflowValidator
 
write(Kryo, Output) - Method in class com.github.seqware.queryengine.util.FSGID
 
write(Kryo, Output) - Method in class com.github.seqware.queryengine.util.SGID
 
writeKeyValueFile(File, Map<String, String>) - Static method in class com.github.seqware.queryengine.system.Utility
Write to output file a tab separated key value file represented by map
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
WS_PASS - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
WS_URL - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
WS_USER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 

X

XmlizeFileSet - Class in net.sourceforge.seqware.common.model.adapters
 
XmlizeFileSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
 
XmlizeIUSSortedSet - Class in net.sourceforge.seqware.common.model.adapters
 
XmlizeIUSSortedSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
 
XmlizeLaneSortedSet - Class in net.sourceforge.seqware.common.model.adapters
 
XmlizeLaneSortedSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
 
XmlizeXML - Class in net.sourceforge.seqware.common.model.adapters
 
XmlizeXML() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeXML
 
XmlTools - Class in net.sourceforge.seqware.common.util.xmltools
 
XmlTools() - Constructor for class net.sourceforge.seqware.common.util.xmltools.XmlTools
 
xreflink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
 
XSI - Variable in class net.sourceforge.seqware.pipeline.workflowV2.pegasus.object.PegasusAbstract
 

Y

YanHuangGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
 
YanHuangGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.YanHuangGenomeVariantImportWorker
 

Z

Zip - Class in net.sourceforge.seqware.pipeline.tools
 
Zip() - Constructor for class net.sourceforge.seqware.pipeline.tools.Zip
 
zipDirectoryRecursive(File, File, String, boolean, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
zipDirectoryRecursiveOld(File, File, String, boolean, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
ZipFileUtil - Class in net.sourceforge.solexatools.util
 
ZipFileUtil() - Constructor for class net.sourceforge.solexatools.util.ZipFileUtil
 
zipListFileRecursiveOld(List<File>, File, String, String, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
zygosity - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 

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